data_6XKO # _entry.id 6XKO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 6XKO pdb_00006xko 10.2210/pdb6xko/pdb WWPDB D_1000250311 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6XKO _pdbx_database_status.recvd_initial_deposition_date 2020-06-26 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Srivastava, K.Y.' 1 0000-0001-9091-9851 'Jenkins, J.L.' 2 0000-0003-2548-3275 'Wedekind, J.E.' 3 0000-0002-4269-4229 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'New insights into Class III PreQ1 metabolite binding' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Srivastava, K.Y.' 1 0000-0001-9091-9851 primary 'Jenkins, J.L.' 2 0000-0003-2548-3275 primary 'Wedekind, J.E.' 3 0000-0002-4269-4229 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 6XKO _cell.details ? _cell.formula_units_Z ? _cell.length_a 83.798 _cell.length_a_esd ? _cell.length_b 83.798 _cell.length_b_esd ? _cell.length_c 277.104 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XKO _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'Class III PreQ1 riboswitch' 32655.254 1 ? A84G ? ? 2 non-polymer syn 7-DEAZA-7-AMINOMETHYL-GUANINE 179.179 1 ? ? ? ? 3 water nat water 18.015 9 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;(GTP)AGCAACUUAGGAUUUUAGGCUCCCCGGCGUGUCUCGAACCAUGCCGGGCCAAACCCAUAGGGCUGGCGGUCCCUG UGCGGUCGAAAUUCAUCCGCCGGAG ; _entity_poly.pdbx_seq_one_letter_code_can ;GAGCAACUUAGGAUUUUAGGCUCCCCGGCGUGUCUCGAACCAUGCCGGGCCAAACCCAUAGGGCUGGCGGUCCCUGUGCG GUCGAAAUUCAUCCGCCGGAG ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GTP n 1 2 A n 1 3 G n 1 4 C n 1 5 A n 1 6 A n 1 7 C n 1 8 U n 1 9 U n 1 10 A n 1 11 G n 1 12 G n 1 13 A n 1 14 U n 1 15 U n 1 16 U n 1 17 U n 1 18 A n 1 19 G n 1 20 G n 1 21 C n 1 22 U n 1 23 C n 1 24 C n 1 25 C n 1 26 C n 1 27 G n 1 28 G n 1 29 C n 1 30 G n 1 31 U n 1 32 G n 1 33 U n 1 34 C n 1 35 U n 1 36 C n 1 37 G n 1 38 A n 1 39 A n 1 40 C n 1 41 C n 1 42 A n 1 43 U n 1 44 G n 1 45 C n 1 46 C n 1 47 G n 1 48 G n 1 49 G n 1 50 C n 1 51 C n 1 52 A n 1 53 A n 1 54 A n 1 55 C n 1 56 C n 1 57 C n 1 58 A n 1 59 U n 1 60 A n 1 61 G n 1 62 G n 1 63 G n 1 64 C n 1 65 U n 1 66 G n 1 67 G n 1 68 C n 1 69 G n 1 70 G n 1 71 U n 1 72 C n 1 73 C n 1 74 C n 1 75 U n 1 76 G n 1 77 U n 1 78 G n 1 79 C n 1 80 G n 1 81 G n 1 82 U n 1 83 C n 1 84 G n 1 85 A n 1 86 A n 1 87 A n 1 88 U n 1 89 U n 1 90 C n 1 91 A n 1 92 U n 1 93 C n 1 94 C n 1 95 G n 1 96 C n 1 97 C n 1 98 G n 1 99 G n 1 100 A n 1 101 G n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 101 _pdbx_entity_src_syn.organism_scientific 'Faecalibacterium prausnitzii' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 853 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6XKO _struct_ref.pdbx_db_accession 6XKO _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6XKO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 101 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6XKO _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 101 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 101 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HOH non-polymer . WATER ? 'H2 O' 18.015 PRF non-polymer . 7-DEAZA-7-AMINOMETHYL-GUANINE ? 'C7 H9 N5 O' 179.179 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6XKO _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 4.30 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 71.40 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '80% Tacsimate pH 7.0, 10 mM magnesium acetate, 6 mM cobalt haxammine, 1 mM spermine' _exptl_crystal_grow.pdbx_pH_range 7.0 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-10-08 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.62790 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'CHESS BEAMLINE A1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.62790 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline A1 _diffrn_source.pdbx_synchrotron_site CHESS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6XKO _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.75 _reflns.d_resolution_low 44.05 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 15744 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.1 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 8.7 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 22.7 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all 0.034 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.75 _reflns_shell.d_res_low 2.85 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.7 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1535 _reflns_shell.percent_possible_all 99.2 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 9.0 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all 0.43 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 191.250 _refine.B_iso_mean 85.9 _refine.B_iso_min 35.180 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 6XKO _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.7500 _refine.ls_d_res_low 44.0500 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 15744 _refine.ls_number_reflns_R_free 1569 _refine.ls_number_reflns_R_work 14175 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.1300 _refine.ls_percent_reflns_R_free 9.9700 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2097 _refine.ls_R_factor_R_free 0.2233 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2081 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.340 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_starting_model 4RZD _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 24.1600 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.3900 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 2.7500 _refine_hist.d_res_low 44.0500 _refine_hist.number_atoms_solvent 9 _refine_hist.number_atoms_total 2066 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 95 _refine_hist.pdbx_B_iso_mean_ligand 65.74 _refine_hist.pdbx_B_iso_mean_solvent 57.65 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 2035 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.006 ? ? 2284 'X-RAY DIFFRACTION' ? f_angle_d 0.840 ? ? 3555 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 13.787 ? ? 1137 'X-RAY DIFFRACTION' ? f_chiral_restr 0.036 ? ? 474 'X-RAY DIFFRACTION' ? f_plane_restr 0.007 ? ? 96 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.7500 2.8400 1384 . 140 1244 99.0000 . . . 0.4292 0.0000 0.4061 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 2.8400 2.9400 1379 . 141 1238 99.0000 . . . 0.3654 0.0000 0.3685 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 2.9400 3.0600 1395 . 146 1249 99.0000 . . . 0.3135 0.0000 0.2825 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 3.0600 3.2000 1390 . 129 1261 99.0000 . . . 0.2373 0.0000 0.2284 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 3.2000 3.3600 1405 . 141 1264 99.0000 . . . 0.2210 0.0000 0.2164 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 3.3600 3.5700 1392 . 141 1251 99.0000 . . . 0.2505 0.0000 0.2153 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 3.5700 3.8500 1431 . 143 1288 99.0000 . . . 0.1972 0.0000 0.1816 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 3.8500 4.2400 1430 . 139 1291 100.0000 . . . 0.1848 0.0000 0.1701 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 4.2400 4.8500 1458 . 139 1319 100.0000 . . . 0.2112 0.0000 0.1753 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 4.8500 6.1100 1496 . 149 1347 100.0000 . . . 0.1674 0.0000 0.1816 . . . . . . . 11 . . . 'X-RAY DIFFRACTION' 6.1100 44.0500 1584 . 161 1423 98.0000 . . . 0.2230 0.0000 0.1968 . . . . . . . 11 . . . # _struct.entry_id 6XKO _struct.title 'Class III PreQ1 riboswitch mutant A84G' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6XKO _struct_keywords.text ;PREQ1, QUEUOSINE, THREE-WAY HELICAL JUNCTION, APTAMER, METABOLITE, TRANSLATIONAL REGULATION, HL(OUT)-TYPE PSEUDOKNOT, RIBOSWITCH, RNA ; _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GTP 1 "O3'" ? ? ? 1_555 A A 2 P ? ? A GTP 1 A A 2 1_555 ? ? ? ? ? ? ? 1.566 ? ? hydrog1 hydrog ? ? A GTP 1 N1 ? ? ? 1_555 A C 23 N3 ? ? A GTP 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A GTP 1 N2 ? ? ? 1_555 A C 23 O2 ? ? A GTP 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A GTP 1 O6 ? ? ? 1_555 A C 23 N4 ? ? A GTP 1 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 2 N1 ? ? ? 1_555 A U 22 N3 ? ? A A 2 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 2 N6 ? ? ? 1_555 A U 22 O4 ? ? A A 2 A U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 3 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 4 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 4 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 4 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A G 19 N1 ? ? A A 5 A G 19 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A G 19 O6 ? ? A A 5 A G 19 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog14 hydrog ? ? A A 6 N1 ? ? ? 1_555 A A 18 N6 ? ? A A 6 A A 18 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 85 N7 ? ? A U 8 A A 85 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog16 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 85 N6 ? ? A U 8 A A 85 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog17 hydrog ? ? A U 9 N3 ? ? ? 1_555 A A 86 N7 ? ? A U 9 A A 86 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog18 hydrog ? ? A U 9 O4 ? ? ? 1_555 A A 86 N6 ? ? A U 9 A A 86 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog19 hydrog ? ? A A 10 N1 ? ? ? 1_555 A A 87 N6 ? ? A A 10 A A 87 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog20 hydrog ? ? A A 10 N6 ? ? ? 1_555 A A 87 N7 ? ? A A 10 A A 87 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog21 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 90 N3 ? ? A G 11 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 90 O2 ? ? A G 11 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 90 N4 ? ? A G 11 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 A U 89 O2 ? ? A G 12 A U 89 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog25 hydrog ? ? A G 12 O6 ? ? ? 1_555 A U 89 N3 ? ? A G 12 A U 89 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog26 hydrog ? ? A A 13 N1 ? ? ? 1_555 A U 88 N3 ? ? A A 13 A U 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 13 N6 ? ? ? 1_555 A U 88 O4 ? ? A A 13 A U 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 87 N1 ? ? A U 14 A A 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 87 N6 ? ? A U 14 A A 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 15 N3 ? ? ? 1_555 A A 86 N1 ? ? A U 15 A A 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 15 O4 ? ? ? 1_555 A A 86 N6 ? ? A U 15 A A 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 16 N3 ? ? ? 1_555 A A 85 N1 ? ? A U 16 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A U 16 O4 ? ? ? 1_555 A A 85 N6 ? ? A U 16 A A 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A U 17 O2 ? ? ? 1_555 A G 84 N2 ? ? A U 17 A G 84 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog35 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 49 N1 ? ? A C 24 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 49 O6 ? ? A C 24 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 49 N2 ? ? A C 24 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 48 N1 ? ? A C 25 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 48 O6 ? ? A C 25 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 48 N2 ? ? A C 25 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 26 N3 ? ? ? 1_555 A G 47 N1 ? ? A C 26 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 26 N4 ? ? ? 1_555 A G 47 O6 ? ? A C 26 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 26 O2 ? ? ? 1_555 A G 47 N2 ? ? A C 26 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 27 N1 ? ? ? 1_555 A C 46 N3 ? ? A G 27 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 27 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 27 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 27 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 27 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 28 N1 ? ? ? 1_555 A C 45 N3 ? ? A G 28 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 28 N2 ? ? ? 1_555 A C 45 O2 ? ? A G 28 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 28 O6 ? ? ? 1_555 A C 45 N4 ? ? A G 28 A C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 29 N3 ? ? ? 1_555 A G 44 N1 ? ? A C 29 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 29 N4 ? ? ? 1_555 A G 44 O6 ? ? A C 29 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 29 O2 ? ? ? 1_555 A G 44 N2 ? ? A C 29 A G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 30 N1 ? ? ? 1_555 A U 43 O2 ? ? A G 30 A U 43 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog54 hydrog ? ? A G 30 O6 ? ? ? 1_555 A U 43 N3 ? ? A G 30 A U 43 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog55 hydrog ? ? A U 31 N3 ? ? ? 1_555 A A 42 N1 ? ? A U 31 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A U 31 O4 ? ? ? 1_555 A A 42 N6 ? ? A U 31 A A 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 32 N1 ? ? ? 1_555 A C 41 N3 ? ? A G 32 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 32 N2 ? ? ? 1_555 A C 41 O2 ? ? A G 32 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 32 O6 ? ? ? 1_555 A C 41 N4 ? ? A G 32 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A A 53 N6 ? ? ? 1_555 A C 83 O2 ? ? A A 53 A C 83 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog61 hydrog ? ? A A 54 N1 ? ? ? 1_555 A U 82 N3 ? ? A A 54 A U 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A A 54 N6 ? ? ? 1_555 A U 82 O4 ? ? A A 54 A U 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 55 N3 ? ? ? 1_555 A G 81 N1 ? ? A C 55 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 55 N4 ? ? ? 1_555 A G 81 O6 ? ? A C 55 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A C 55 O2 ? ? ? 1_555 A G 81 N2 ? ? A C 55 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 56 N3 ? ? ? 1_555 A G 80 N1 ? ? A C 56 A G 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 56 N4 ? ? ? 1_555 A G 80 O6 ? ? A C 56 A G 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 56 O2 ? ? ? 1_555 A G 80 N2 ? ? A C 56 A G 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A C 57 N3 ? ? ? 1_555 A G 78 N1 ? ? A C 57 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A C 57 N4 ? ? ? 1_555 A G 78 O6 ? ? A C 57 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A C 57 O2 ? ? ? 1_555 A G 78 N2 ? ? A C 57 A G 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A A 58 N1 ? ? ? 1_555 A U 77 N3 ? ? A A 58 A U 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A A 58 N6 ? ? ? 1_555 A U 77 O4 ? ? A A 58 A U 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A U 59 N3 ? ? ? 1_555 A G 76 O6 ? ? A U 59 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog75 hydrog ? ? A U 59 O2 ? ? ? 1_555 A G 76 N1 ? ? A U 59 A G 76 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog76 hydrog ? ? A A 60 N1 ? ? ? 1_555 A U 75 N3 ? ? A A 60 A U 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A A 60 N6 ? ? ? 1_555 A U 75 O4 ? ? A A 60 A U 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A G 61 N1 ? ? ? 1_555 A C 74 N3 ? ? A G 61 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? A G 61 N2 ? ? ? 1_555 A C 74 O2 ? ? A G 61 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? A G 61 O6 ? ? ? 1_555 A C 74 N4 ? ? A G 61 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? A G 62 N1 ? ? ? 1_555 A C 73 N3 ? ? A G 62 A C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? A G 62 N2 ? ? ? 1_555 A C 73 O2 ? ? A G 62 A C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? A G 62 O6 ? ? ? 1_555 A C 73 N4 ? ? A G 62 A C 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? A G 63 N1 ? ? ? 1_555 A C 72 N3 ? ? A G 63 A C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? A G 63 N2 ? ? ? 1_555 A C 72 O2 ? ? A G 63 A C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? A G 63 O6 ? ? ? 1_555 A C 72 N4 ? ? A G 63 A C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id PRF _struct_site.pdbx_auth_seq_id 201 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 7 _struct_site.details 'binding site for residue PRF A 201' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 7 C A 7 ? C A 7 . ? 1_555 ? 2 AC1 7 U A 8 ? U A 8 . ? 1_555 ? 3 AC1 7 U A 17 ? U A 17 . ? 1_555 ? 4 AC1 7 A A 18 ? A A 18 . ? 1_555 ? 5 AC1 7 G A 84 ? G A 84 . ? 1_555 ? 6 AC1 7 A A 85 ? A A 85 . ? 1_555 ? 7 AC1 7 HOH C . ? HOH A 302 . ? 1_555 ? # _atom_sites.entry_id 6XKO _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.011933 _atom_sites.fract_transf_matrix[1][2] 0.006890 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.013780 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.003609 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GTP 1 1 1 GTP GTP A . n A 1 2 A 2 2 2 A A A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 A 5 5 5 A A A . n A 1 6 A 6 6 6 A A A . n A 1 7 C 7 7 7 C C A . n A 1 8 U 8 8 8 U U A . n A 1 9 U 9 9 9 U U A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 G 12 12 12 G G A . n A 1 13 A 13 13 13 A A A . n A 1 14 U 14 14 14 U U A . n A 1 15 U 15 15 15 U U A . n A 1 16 U 16 16 16 U U A . n A 1 17 U 17 17 17 U U A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 G 20 20 20 G G A . n A 1 21 C 21 21 21 C C A . n A 1 22 U 22 22 22 U U A . n A 1 23 C 23 23 23 C C A . n A 1 24 C 24 24 24 C C A . n A 1 25 C 25 25 25 C C A . n A 1 26 C 26 26 26 C C A . n A 1 27 G 27 27 27 G G A . n A 1 28 G 28 28 28 G G A . n A 1 29 C 29 29 29 C C A . n A 1 30 G 30 30 30 G G A . n A 1 31 U 31 31 31 U U A . n A 1 32 G 32 32 32 G G A . n A 1 33 U 33 33 ? ? ? A . n A 1 34 C 34 34 ? ? ? A . n A 1 35 U 35 35 ? ? ? A . n A 1 36 C 36 36 ? ? ? A . n A 1 37 G 37 37 ? ? ? A . n A 1 38 A 38 38 ? ? ? A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 C 41 41 41 C C A . n A 1 42 A 42 42 42 A A A . n A 1 43 U 43 43 43 U U A . n A 1 44 G 44 44 44 G G A . n A 1 45 C 45 45 45 C C A . n A 1 46 C 46 46 46 C C A . n A 1 47 G 47 47 47 G G A . n A 1 48 G 48 48 48 G G A . n A 1 49 G 49 49 49 G G A . n A 1 50 C 50 50 50 C C A . n A 1 51 C 51 51 51 C C A . n A 1 52 A 52 52 52 A A A . n A 1 53 A 53 53 53 A A A . n A 1 54 A 54 54 54 A A A . n A 1 55 C 55 55 55 C C A . n A 1 56 C 56 56 56 C C A . n A 1 57 C 57 57 57 C C A . n A 1 58 A 58 58 58 A A A . n A 1 59 U 59 59 59 U U A . n A 1 60 A 60 60 60 A A A . n A 1 61 G 61 61 61 G G A . n A 1 62 G 62 62 62 G G A . n A 1 63 G 63 63 63 G G A . n A 1 64 C 64 64 64 C C A . n A 1 65 U 65 65 65 U U A . n A 1 66 G 66 66 66 G G A . n A 1 67 G 67 67 67 G G A . n A 1 68 C 68 68 68 C C A . n A 1 69 G 69 69 69 G G A . n A 1 70 G 70 70 70 G G A . n A 1 71 U 71 71 71 U U A . n A 1 72 C 72 72 72 C C A . n A 1 73 C 73 73 73 C C A . n A 1 74 C 74 74 74 C C A . n A 1 75 U 75 75 75 U U A . n A 1 76 G 76 76 76 G G A . n A 1 77 U 77 77 77 U U A . n A 1 78 G 78 78 78 G G A . n A 1 79 C 79 79 79 C C A . n A 1 80 G 80 80 80 G G A . n A 1 81 G 81 81 81 G G A . n A 1 82 U 82 82 82 U U A . n A 1 83 C 83 83 83 C C A . n A 1 84 G 84 84 84 G G A . n A 1 85 A 85 85 85 A A A . n A 1 86 A 86 86 86 A A A . n A 1 87 A 87 87 87 A A A . n A 1 88 U 88 88 88 U U A . n A 1 89 U 89 89 89 U U A . n A 1 90 C 90 90 90 C C A . n A 1 91 A 91 91 91 A A A . n A 1 92 U 92 92 92 U U A . n A 1 93 C 93 93 93 C C A . n A 1 94 C 94 94 94 C C A . n A 1 95 G 95 95 95 G G A . n A 1 96 C 96 96 96 C C A . n A 1 97 C 97 97 97 C C A . n A 1 98 G 98 98 98 G G A . n A 1 99 G 99 99 99 G G A . n A 1 100 A 100 100 100 A A A . n A 1 101 G 101 101 101 G G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PRF 1 201 201 PRF PRF A . C 3 HOH 1 301 1 HOH HOH A . C 3 HOH 2 302 11 HOH HOH A . C 3 HOH 3 303 23 HOH HOH A . C 3 HOH 4 304 20 HOH HOH A . C 3 HOH 5 305 24 HOH HOH A . C 3 HOH 6 306 6 HOH HOH A . C 3 HOH 7 307 17 HOH HOH A . C 3 HOH 8 308 25 HOH HOH A . C 3 HOH 9 309 14 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2021-12-29 2 'Structure model' 1 1 2023-10-18 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined -4.3181 58.3368 100.7618 0.8818 ? 0.1914 ? -0.0755 ? 0.9597 ? 0.1228 ? 1.3132 ? 0.1332 ? -0.1031 ? -0.0917 ? 0.1579 ? 0.1083 ? 0.0808 ? 0.3629 ? -0.7415 ? -0.9172 ? 0.3673 ? 0.1288 ? 0.9174 ? 0.5646 ? -1.2320 ? -0.0003 ? 2 'X-RAY DIFFRACTION' ? refined 9.8115 52.8007 98.3401 0.7271 ? 0.1564 ? -0.0384 ? 0.7311 ? -0.0578 ? 0.6054 ? 0.1714 ? -0.0835 ? -0.0910 ? 0.4464 ? -0.0090 ? 0.1013 ? -0.4776 ? 0.6588 ? 0.2054 ? -0.0327 ? 0.0974 ? 0.2927 ? 0.3508 ? 0.3495 ? -0.0006 ? 3 'X-RAY DIFFRACTION' ? refined 14.7846 48.0768 111.9935 1.0127 ? 0.2270 ? -0.1316 ? 0.6355 ? -0.0591 ? 0.8461 ? 0.2850 ? -0.1799 ? -0.0224 ? 0.1202 ? 0.0496 ? 0.1672 ? 0.4763 ? 0.7098 ? -0.6611 ? -0.2298 ? -0.1778 ? 0.2403 ? 1.0620 ? 0.7911 ? 0.0085 ? 4 'X-RAY DIFFRACTION' ? refined 13.1005 33.5723 110.6092 1.1905 ? 0.2422 ? 0.0464 ? 0.7530 ? -0.0093 ? 1.3676 ? 2.2102 ? -0.7056 ? 2.1011 ? 0.5037 ? 0.1738 ? 4.5543 ? -0.4566 ? -1.1942 ? -0.8595 ? 1.8049 ? 0.4986 ? -0.5641 ? 0.2844 ? -1.0839 ? 0.1939 ? 5 'X-RAY DIFFRACTION' ? refined 28.5772 34.4368 103.7958 0.6447 ? 0.2702 ? 0.0133 ? 0.5384 ? 0.0625 ? 0.7947 ? 0.9317 ? -0.3042 ? -0.3428 ? 0.7698 ? 0.6749 ? 0.8167 ? -0.2097 ? 0.1200 ? -0.1400 ? -0.6035 ? 0.2559 ? 1.0848 ? 0.2028 ? -0.3113 ? -0.0028 ? 6 'X-RAY DIFFRACTION' ? refined 39.9712 44.4282 95.6157 0.9933 ? 0.0433 ? 0.1025 ? 0.6983 ? 0.1093 ? 0.8149 ? 0.1872 ? -0.2391 ? -0.0976 ? 0.3190 ? 0.1153 ? 0.0532 ? 0.8839 ? 0.4300 ? 1.4664 ? -0.7377 ? 0.0074 ? 0.5801 ? 0.0118 ? 0.1224 ? 0.0027 ? 7 'X-RAY DIFFRACTION' ? refined 50.9073 31.9928 92.1649 0.8098 ? 0.1316 ? -0.1564 ? 1.0045 ? 0.1281 ? 0.8705 ? 0.4646 ? 0.1299 ? -0.2935 ? 0.1879 ? -0.0576 ? 0.4686 ? -0.3705 ? -0.8521 ? -0.5045 ? 0.9109 ? 0.1882 ? 0.1048 ? -0.8593 ? 1.3723 ? -0.0009 ? 8 'X-RAY DIFFRACTION' ? refined 67.1628 25.9114 90.8870 1.0150 ? 0.1774 ? -0.2001 ? 1.3748 ? 0.2712 ? 1.8216 ? 0.2424 ? 0.2302 ? 0.0037 ? 0.3323 ? 0.1597 ? 0.2127 ? -0.5023 ? -0.8682 ? -0.7908 ? 0.1150 ? 0.2554 ? -0.8626 ? 0.3756 ? 1.1785 ? -0.0084 ? 9 'X-RAY DIFFRACTION' ? refined 36.6574 39.0231 122.5312 1.1508 ? -0.0138 ? 0.2108 ? 0.8802 ? 0.0007 ? 0.7825 ? 1.4338 ? 1.2561 ? 0.7046 ? 1.2422 ? 0.3850 ? 0.6971 ? 0.1719 ? 0.1464 ? 1.4717 ? 0.5869 ? 0.2020 ? 0.4100 ? -0.8541 ? -1.5836 ? 0.0106 ? 10 'X-RAY DIFFRACTION' ? refined 39.0612 28.6523 107.0918 0.7516 ? 0.1872 ? 0.0062 ? 0.6827 ? 0.0367 ? 0.5352 ? 0.5794 ? -0.4624 ? -0.3590 ? 0.5651 ? 0.1044 ? 0.3878 ? 0.3122 ? -0.0685 ? -0.1562 ? -0.4389 ? 0.1141 ? -0.0531 ? -0.4524 ? 0.3890 ? 0.0011 ? 11 'X-RAY DIFFRACTION' ? refined 41.2226 36.2468 99.3037 0.8637 ? 0.0650 ? -0.0313 ? 0.8880 ? 0.0926 ? 0.6331 ? 0.6076 ? -0.0058 ? -0.1190 ? 0.1273 ? 0.1405 ? 0.1710 ? 0.3197 ? -0.0594 ? 0.2459 ? 0.1285 ? 0.0209 ? -0.1738 ? 0.0849 ? 0.6578 ? 0.0002 ? 12 'X-RAY DIFFRACTION' ? refined 33.0549 36.5747 111.1560 0.7442 ? 0.1065 ? 0.0828 ? 0.5543 ? -0.0084 ? 0.6834 ? 0.1157 ? 0.0923 ? -0.0658 ? 0.0680 ? -0.0575 ? 0.2945 ? -0.5670 ? -0.4033 ? 0.6967 ? -0.4894 ? 0.5597 ? 0.4424 ? -0.0641 ? 0.4864 ? 0.0034 ? 13 'X-RAY DIFFRACTION' ? refined 34.9390 31.7207 126.2997 0.9408 ? 0.1202 ? 0.1662 ? 0.6466 ? -0.0954 ? 0.7394 ? 0.6017 ? -0.3560 ? -0.0796 ? 0.5505 ? 0.1158 ? 0.0234 ? 0.1934 ? -0.2777 ? 0.6521 ? 0.3360 ? 0.4153 ? 0.2521 ? -0.4811 ? 0.1380 ? -0.0019 ? 14 'X-RAY DIFFRACTION' ? refined 23.7309 31.0576 142.0900 1.4376 ? 0.1317 ? 0.1850 ? 1.4806 ? 0.3628 ? 1.0744 ? 0.6267 ? -0.7112 ? 0.4974 ? 0.8069 ? -0.5635 ? 0.3940 ? 0.7519 ? -1.6300 ? -0.7041 ? 0.2223 ? 0.8001 ? 1.3120 ? 0.2675 ? -0.0064 ? 0.0268 ? 15 'X-RAY DIFFRACTION' ? refined 30.5809 29.9275 151.2861 1.6548 ? 0.1593 ? 0.2181 ? 2.2068 ? 0.1315 ? 1.3683 ? 0.4205 ? 0.1660 ? -0.0748 ? 0.1661 ? 0.1169 ? 0.2241 ? 0.3028 ? -1.2413 ? 0.7133 ? -0.3479 ? 1.0863 ? 1.3168 ? -1.0351 ? -1.2609 ? 0.0021 ? 16 'X-RAY DIFFRACTION' ? refined 35.2556 29.0617 144.0676 1.3663 ? 0.1259 ? 0.0164 ? 1.4983 ? -0.0131 ? 0.8833 ? 0.2272 ? 0.1225 ? -0.2198 ? 0.1631 ? -0.2804 ? 0.4784 ? -0.2396 ? -0.4447 ? 0.6519 ? -0.6379 ? -0.1847 ? -0.0692 ? -1.4885 ? -2.2031 ? 0.0027 ? 17 'X-RAY DIFFRACTION' ? refined 24.8785 31.1470 131.7613 1.1999 ? -0.0105 ? 0.0450 ? 0.9829 ? 0.0608 ? 1.0662 ? 0.1621 ? 0.0281 ? 0.0188 ? 0.0133 ? -0.0006 ? 0.0028 ? 1.1947 ? 0.9568 ? -1.3166 ? 0.3238 ? -0.4811 ? 0.9691 ? -0.0104 ? 1.0318 ? 0.0042 ? 18 'X-RAY DIFFRACTION' ? refined 24.1698 38.8308 111.6481 0.8980 ? 0.2245 ? 0.0415 ? 0.7774 ? 0.1028 ? 0.9102 ? 0.3142 ? 0.2757 ? 0.0873 ? 0.2403 ? 0.0800 ? 0.0702 ? 0.3306 ? -0.0315 ? 0.1187 ? 0.3195 ? -0.4839 ? 0.8807 ? -0.2288 ? 0.6112 ? 0.0017 ? 19 'X-RAY DIFFRACTION' ? refined 9.9148 41.0844 103.9107 0.9122 ? 0.3016 ? -0.1493 ? 0.8356 ? -0.1736 ? 0.9907 ? 0.8266 ? -0.8761 ? -0.7753 ? 1.1786 ? 0.9691 ? 0.8126 ? -0.2667 ? 1.3218 ? -0.9274 ? 0.8563 ? -0.3527 ? 0.2689 ? 0.6274 ? 0.0723 ? -0.0121 ? 20 'X-RAY DIFFRACTION' ? refined 6.3355 59.6637 105.8743 1.0098 ? 0.2378 ? -0.0590 ? 0.5831 ? 0.0120 ? 0.8077 ? 0.7860 ? -0.0315 ? -0.3862 ? 0.5634 ? 0.2339 ? 0.2718 ? 0.1653 ? 0.1884 ? 0.1887 ? -0.2800 ? -0.2631 ? 0.9302 ? 0.0343 ? -0.3418 ? -0.0002 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 ? ? A 67 ? ? ? A 70 ? ? '(chain A and resid 67:70)' 2 'X-RAY DIFFRACTION' 2 ? ? A 71 ? ? ? A 74 ? ? '(chain A and resid 71:74)' 3 'X-RAY DIFFRACTION' 3 ? ? A 75 ? ? ? A 78 ? ? '(chain A and resid 75:78)' 4 'X-RAY DIFFRACTION' 4 ? ? A 79 ? ? ? A 83 ? ? '(chain A and resid 79:83)' 5 'X-RAY DIFFRACTION' 5 ? ? A 84 ? ? ? A 87 ? ? '(chain A and resid 84:87)' 6 'X-RAY DIFFRACTION' 6 ? ? A 88 ? ? ? A 91 ? ? '(chain A and resid 88:91)' 7 'X-RAY DIFFRACTION' 7 ? ? A 92 ? ? ? A 95 ? ? '(chain A and resid 92:95)' 8 'X-RAY DIFFRACTION' 8 ? ? A 96 ? ? ? A 101 ? ? '(chain A and resid 96:101)' 9 'X-RAY DIFFRACTION' 9 ? ? A 1 ? ? ? A 4 ? ? '(chain A and resid 1:4)' 10 'X-RAY DIFFRACTION' 10 ? ? A 5 ? ? ? A 9 ? ? '(chain A and resid 5:9)' 11 'X-RAY DIFFRACTION' 11 ? ? A 10 ? ? ? A 14 ? ? '(chain A and resid 10:14)' 12 'X-RAY DIFFRACTION' 12 ? ? A 15 ? ? ? A 18 ? ? '(chain A and resid 15:18)' 13 'X-RAY DIFFRACTION' 13 ? ? A 19 ? ? ? A 26 ? ? '(chain A and resid 19:26)' 14 'X-RAY DIFFRACTION' 14 ? ? A 27 ? ? ? A 30 ? ? '(chain A and resid 27:30)' 15 'X-RAY DIFFRACTION' 15 ? ? A 31 ? ? ? A 40 ? ? '(chain A and resid 31:40)' 16 'X-RAY DIFFRACTION' 16 ? ? A 41 ? ? ? A 44 ? ? '(chain A and resid 41:44)' 17 'X-RAY DIFFRACTION' 17 ? ? A 45 ? ? ? A 49 ? ? '(chain A and resid 45:49)' 18 'X-RAY DIFFRACTION' 18 ? ? A 50 ? ? ? A 54 ? ? '(chain A and resid 50:54)' 19 'X-RAY DIFFRACTION' 19 ? ? A 55 ? ? ? A 58 ? ? '(chain A and resid 55:58)' 20 'X-RAY DIFFRACTION' 20 ? ? A 59 ? ? ? A 66 ? ? '(chain A and resid 59:66)' # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1_3660 1 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v708c 3 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? v708c 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1_3660 5 # _pdbx_entry_details.entry_id 6XKO _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'Adenine 84 mutated to guanine' # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A GTP 1 ? ? "O3'" A GTP 1 ? ? P A A 2 ? ? 97.04 119.70 -22.66 1.20 Y 2 1 "O3'" A GTP 1 ? ? P A A 2 ? ? OP2 A A 2 ? ? 138.52 110.50 28.02 1.10 Y 3 1 "O3'" A GTP 1 ? ? P A A 2 ? ? OP1 A A 2 ? ? 85.10 105.20 -20.10 2.20 Y 4 1 C2 A A 18 ? ? N3 A A 18 ? ? C4 A A 18 ? ? 107.58 110.60 -3.02 0.50 N 5 1 C4 A A 18 ? ? C5 A A 18 ? ? N7 A A 18 ? ? 114.29 110.70 3.59 0.50 N 6 1 C5 A A 18 ? ? N7 A A 18 ? ? C8 A A 18 ? ? 99.77 103.90 -4.13 0.50 N # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 33 ? A U 33 2 1 Y 1 A C 34 ? A C 34 3 1 Y 1 A U 35 ? A U 35 4 1 Y 1 A C 36 ? A C 36 5 1 Y 1 A G 37 ? A G 37 6 1 Y 1 A A 38 ? A A 38 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 GTP PG P N N 111 GTP O1G O N N 112 GTP O2G O N N 113 GTP O3G O N N 114 GTP O3B O N N 115 GTP PB P N N 116 GTP O1B O N N 117 GTP O2B O N N 118 GTP O3A O N N 119 GTP PA P N N 120 GTP O1A O N N 121 GTP O2A O N N 122 GTP "O5'" O N N 123 GTP "C5'" C N N 124 GTP "C4'" C N R 125 GTP "O4'" O N N 126 GTP "C3'" C N S 127 GTP "O3'" O N N 128 GTP "C2'" C N R 129 GTP "O2'" O N N 130 GTP "C1'" C N R 131 GTP N9 N Y N 132 GTP C8 C Y N 133 GTP N7 N Y N 134 GTP C5 C Y N 135 GTP C6 C N N 136 GTP O6 O N N 137 GTP N1 N N N 138 GTP C2 C N N 139 GTP N2 N N N 140 GTP N3 N N N 141 GTP C4 C Y N 142 GTP HOG2 H N N 143 GTP HOG3 H N N 144 GTP HOB2 H N N 145 GTP HOA2 H N N 146 GTP "H5'" H N N 147 GTP "H5''" H N N 148 GTP "H4'" H N N 149 GTP "H3'" H N N 150 GTP "HO3'" H N N 151 GTP "H2'" H N N 152 GTP "HO2'" H N N 153 GTP "H1'" H N N 154 GTP H8 H N N 155 GTP HN1 H N N 156 GTP HN21 H N N 157 GTP HN22 H N N 158 HOH O O N N 159 HOH H1 H N N 160 HOH H2 H N N 161 PRF N1 N N N 162 PRF C2 C N N 163 PRF N3 N N N 164 PRF C4 C Y N 165 PRF C5 C Y N 166 PRF C6 C N N 167 PRF O6 O N N 168 PRF C7 C Y N 169 PRF C10 C N N 170 PRF N11 N N N 171 PRF C8 C Y N 172 PRF N9 N Y N 173 PRF N2 N N N 174 PRF H91 H N N 175 PRF H101 H N N 176 PRF H102 H N N 177 PRF H111 H N N 178 PRF H112 H N N 179 PRF H81 H N N 180 PRF HN91 H N N 181 PRF HN21 H N N 182 PRF HN22 H N N 183 U OP3 O N N 184 U P P N N 185 U OP1 O N N 186 U OP2 O N N 187 U "O5'" O N N 188 U "C5'" C N N 189 U "C4'" C N R 190 U "O4'" O N N 191 U "C3'" C N S 192 U "O3'" O N N 193 U "C2'" C N R 194 U "O2'" O N N 195 U "C1'" C N R 196 U N1 N N N 197 U C2 C N N 198 U O2 O N N 199 U N3 N N N 200 U C4 C N N 201 U O4 O N N 202 U C5 C N N 203 U C6 C N N 204 U HOP3 H N N 205 U HOP2 H N N 206 U "H5'" H N N 207 U "H5''" H N N 208 U "H4'" H N N 209 U "H3'" H N N 210 U "HO3'" H N N 211 U "H2'" H N N 212 U "HO2'" H N N 213 U "H1'" H N N 214 U H3 H N N 215 U H5 H N N 216 U H6 H N N 217 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 GTP PG O1G doub N N 116 GTP PG O2G sing N N 117 GTP PG O3G sing N N 118 GTP PG O3B sing N N 119 GTP O2G HOG2 sing N N 120 GTP O3G HOG3 sing N N 121 GTP O3B PB sing N N 122 GTP PB O1B doub N N 123 GTP PB O2B sing N N 124 GTP PB O3A sing N N 125 GTP O2B HOB2 sing N N 126 GTP O3A PA sing N N 127 GTP PA O1A doub N N 128 GTP PA O2A sing N N 129 GTP PA "O5'" sing N N 130 GTP O2A HOA2 sing N N 131 GTP "O5'" "C5'" sing N N 132 GTP "C5'" "C4'" sing N N 133 GTP "C5'" "H5'" sing N N 134 GTP "C5'" "H5''" sing N N 135 GTP "C4'" "O4'" sing N N 136 GTP "C4'" "C3'" sing N N 137 GTP "C4'" "H4'" sing N N 138 GTP "O4'" "C1'" sing N N 139 GTP "C3'" "O3'" sing N N 140 GTP "C3'" "C2'" sing N N 141 GTP "C3'" "H3'" sing N N 142 GTP "O3'" "HO3'" sing N N 143 GTP "C2'" "O2'" sing N N 144 GTP "C2'" "C1'" sing N N 145 GTP "C2'" "H2'" sing N N 146 GTP "O2'" "HO2'" sing N N 147 GTP "C1'" N9 sing N N 148 GTP "C1'" "H1'" sing N N 149 GTP N9 C8 sing Y N 150 GTP N9 C4 sing Y N 151 GTP C8 N7 doub Y N 152 GTP C8 H8 sing N N 153 GTP N7 C5 sing Y N 154 GTP C5 C6 sing N N 155 GTP C5 C4 doub Y N 156 GTP C6 O6 doub N N 157 GTP C6 N1 sing N N 158 GTP N1 C2 sing N N 159 GTP N1 HN1 sing N N 160 GTP C2 N2 sing N N 161 GTP C2 N3 doub N N 162 GTP N2 HN21 sing N N 163 GTP N2 HN22 sing N N 164 GTP N3 C4 sing N N 165 HOH O H1 sing N N 166 HOH O H2 sing N N 167 PRF N1 C2 sing N N 168 PRF N1 C6 sing N N 169 PRF N1 H91 sing N N 170 PRF C2 N3 doub N N 171 PRF C2 N2 sing N N 172 PRF N3 C4 sing N N 173 PRF C4 C5 doub Y N 174 PRF C4 N9 sing Y N 175 PRF C5 C6 sing N N 176 PRF C5 C7 sing Y N 177 PRF C6 O6 doub N N 178 PRF C7 C10 sing N N 179 PRF C7 C8 doub Y N 180 PRF C10 N11 sing N N 181 PRF C10 H101 sing N N 182 PRF C10 H102 sing N N 183 PRF N11 H111 sing N N 184 PRF N11 H112 sing N N 185 PRF C8 N9 sing Y N 186 PRF C8 H81 sing N N 187 PRF N9 HN91 sing N N 188 PRF N2 HN21 sing N N 189 PRF N2 HN22 sing N N 190 U OP3 P sing N N 191 U OP3 HOP3 sing N N 192 U P OP1 doub N N 193 U P OP2 sing N N 194 U P "O5'" sing N N 195 U OP2 HOP2 sing N N 196 U "O5'" "C5'" sing N N 197 U "C5'" "C4'" sing N N 198 U "C5'" "H5'" sing N N 199 U "C5'" "H5''" sing N N 200 U "C4'" "O4'" sing N N 201 U "C4'" "C3'" sing N N 202 U "C4'" "H4'" sing N N 203 U "O4'" "C1'" sing N N 204 U "C3'" "O3'" sing N N 205 U "C3'" "C2'" sing N N 206 U "C3'" "H3'" sing N N 207 U "O3'" "HO3'" sing N N 208 U "C2'" "O2'" sing N N 209 U "C2'" "C1'" sing N N 210 U "C2'" "H2'" sing N N 211 U "O2'" "HO2'" sing N N 212 U "C1'" N1 sing N N 213 U "C1'" "H1'" sing N N 214 U N1 C2 sing N N 215 U N1 C6 sing N N 216 U C2 O2 doub N N 217 U C2 N3 sing N N 218 U N3 C4 sing N N 219 U N3 H3 sing N N 220 U C4 O4 doub N N 221 U C4 C5 sing N N 222 U C5 C6 doub N N 223 U C5 H5 sing N N 224 U C6 H6 sing N N 225 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6XKO 'double helix' 6XKO 'a-form double helix' 6XKO 'hairpin loop' 6XKO 'bulge loop' 6XKO 'mismatched base pair' 6XKO 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 11 1_555 A C 90 1_555 -0.359 -0.215 0.224 2.193 -12.701 -1.483 1 A_G11:C90_A A 11 ? A 90 ? 19 1 1 A G 12 1_555 A U 89 1_555 -1.946 -0.457 0.066 -1.200 -13.538 2.027 2 A_G12:U89_A A 12 ? A 89 ? 28 1 1 A A 13 1_555 A U 88 1_555 0.037 -0.035 0.159 -2.600 -11.392 4.749 3 A_A13:U88_A A 13 ? A 88 ? 20 1 1 A U 14 1_555 A A 87 1_555 0.349 -0.356 0.088 2.059 -9.661 -1.765 4 A_U14:A87_A A 14 ? A 87 ? 20 1 1 A U 15 1_555 A A 86 1_555 0.123 0.004 0.246 4.399 -3.678 7.953 5 A_U15:A86_A A 15 ? A 86 ? 20 1 1 A U 16 1_555 A A 85 1_555 -0.040 -0.025 -0.104 3.472 -2.510 4.352 6 A_U16:A85_A A 16 ? A 85 ? 20 1 1 A U 17 1_555 A G 84 1_555 -1.916 -7.899 1.619 -46.264 13.472 -136.475 7 A_U17:G84_A A 17 ? A 84 ? ? 6 1 A A 18 1_555 A A 6 1_555 -2.233 -2.700 0.027 18.122 2.803 124.508 8 A_A18:A6_A A 18 ? A 6 ? ? ? 1 A G 19 1_555 A A 5 1_555 -0.034 1.335 -0.141 5.492 -7.735 -20.946 9 A_G19:A5_A A 19 ? A 5 ? 8 1 1 A G 20 1_555 A C 4 1_555 0.021 -0.252 0.008 -0.390 -12.437 -5.772 10 A_G20:C4_A A 20 ? A 4 ? 19 1 1 A C 21 1_555 A G 3 1_555 0.125 -0.184 0.239 2.255 -16.104 0.423 11 A_C21:G3_A A 21 ? A 3 ? 19 1 1 A U 22 1_555 A A 2 1_555 0.241 0.072 -0.009 5.247 -8.888 0.535 12 A_U22:A2_A A 22 ? A 2 ? 20 1 1 A C 23 1_555 A GTP 1 1_555 0.679 -0.172 0.029 8.071 -8.184 2.642 13 A_C23:GTP1_A A 23 ? A 1 ? 19 1 1 A C 24 1_555 A G 49 1_555 -0.296 -0.039 0.073 6.333 -10.400 1.557 14 A_C24:G49_A A 24 ? A 49 ? 19 1 1 A C 25 1_555 A G 48 1_555 -0.024 -0.270 0.033 13.075 -16.191 -2.626 15 A_C25:G48_A A 25 ? A 48 ? 19 1 1 A C 26 1_555 A G 47 1_555 0.058 -0.180 -0.220 4.334 -9.746 3.324 16 A_C26:G47_A A 26 ? A 47 ? 19 1 1 A G 27 1_555 A C 46 1_555 -0.215 -0.333 -0.078 -1.019 -15.118 -2.948 17 A_G27:C46_A A 27 ? A 46 ? 19 1 1 A G 28 1_555 A C 45 1_555 -0.409 -0.110 -0.564 -12.572 -20.122 1.902 18 A_G28:C45_A A 28 ? A 45 ? 19 1 1 A C 29 1_555 A G 44 1_555 0.097 -0.088 -0.267 -3.145 -16.398 7.067 19 A_C29:G44_A A 29 ? A 44 ? 19 1 1 A G 30 1_555 A U 43 1_555 -1.876 -0.735 0.239 -0.270 -15.695 -4.948 20 A_G30:U43_A A 30 ? A 43 ? 28 1 1 A U 31 1_555 A A 42 1_555 0.320 -0.532 0.493 -7.130 -22.287 1.505 21 A_U31:A42_A A 31 ? A 42 ? 20 1 1 A G 32 1_555 A C 41 1_555 -0.128 0.158 0.222 -0.320 -7.377 1.337 22 A_G32:C41_A A 32 ? A 41 ? 19 1 1 A A 53 1_555 A C 83 1_555 -4.852 -0.903 0.149 8.311 1.364 9.395 23 A_A53:C83_A A 53 ? A 83 ? ? 1 1 A A 54 1_555 A U 82 1_555 -0.535 0.038 -0.051 12.811 -5.181 1.969 24 A_A54:U82_A A 54 ? A 82 ? 20 1 1 A C 55 1_555 A G 81 1_555 0.165 -0.169 -0.695 19.754 -11.844 -0.881 25 A_C55:G81_A A 55 ? A 81 ? 19 1 1 A C 56 1_555 A G 80 1_555 0.261 -0.275 -0.293 2.096 -6.125 3.916 26 A_C56:G80_A A 56 ? A 80 ? 19 1 1 A C 57 1_555 A G 78 1_555 -0.279 -0.049 -0.147 -1.767 -8.600 3.449 27 A_C57:G78_A A 57 ? A 78 ? 19 1 1 A A 58 1_555 A U 77 1_555 -0.239 -0.194 0.361 4.609 -11.410 3.318 28 A_A58:U77_A A 58 ? A 77 ? 20 1 1 A U 59 1_555 A G 76 1_555 1.974 -0.639 0.209 -0.552 -10.582 2.147 29 A_U59:G76_A A 59 ? A 76 ? 28 1 1 A A 60 1_555 A U 75 1_555 -0.204 -0.306 -0.301 -2.757 -5.824 6.100 30 A_A60:U75_A A 60 ? A 75 ? 20 1 1 A G 61 1_555 A C 74 1_555 -0.035 -0.215 -0.475 -6.533 -8.696 -0.495 31 A_G61:C74_A A 61 ? A 74 ? 19 1 1 A G 62 1_555 A C 73 1_555 -0.200 -0.086 -0.336 -16.152 -13.402 2.561 32 A_G62:C73_A A 62 ? A 73 ? 19 1 1 A G 63 1_555 A C 72 1_555 -0.011 -0.233 -0.489 -17.559 -9.457 -1.825 33 A_G63:C72_A A 63 ? A 72 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 11 1_555 A C 90 1_555 A G 12 1_555 A U 89 1_555 -0.028 -1.992 3.059 -3.810 8.837 31.119 -4.875 -0.519 2.405 15.999 6.897 32.538 1 AA_G11G12:U89C90_AA A 11 ? A 90 ? A 12 ? A 89 ? 1 A G 12 1_555 A U 89 1_555 A A 13 1_555 A U 88 1_555 0.002 -1.197 3.258 -2.423 5.769 39.272 -2.411 -0.276 3.053 8.518 3.577 39.748 2 AA_G12A13:U88U89_AA A 12 ? A 89 ? A 13 ? A 88 ? 1 A A 13 1_555 A U 88 1_555 A U 14 1_555 A A 87 1_555 -0.346 -1.419 3.072 0.689 4.012 32.737 -3.122 0.716 2.875 7.083 -1.216 32.982 3 AA_A13U14:A87U88_AA A 13 ? A 88 ? A 14 ? A 87 ? 1 A U 14 1_555 A A 87 1_555 A U 15 1_555 A A 86 1_555 1.282 -1.992 3.097 -0.389 2.619 29.045 -4.479 -2.624 2.893 5.208 0.774 29.163 4 AA_U14U15:A86A87_AA A 14 ? A 87 ? A 15 ? A 86 ? 1 A U 15 1_555 A A 86 1_555 A U 16 1_555 A A 85 1_555 -0.548 -2.468 3.030 0.907 6.547 28.445 -6.094 1.254 2.395 13.101 -1.815 29.187 5 AA_U15U16:A85A86_AA A 15 ? A 86 ? A 16 ? A 85 ? 1 A U 16 1_555 A A 85 1_555 A U 17 1_555 A G 84 1_555 -2.706 1.392 3.579 24.426 16.001 115.135 0.639 1.851 3.296 9.398 -14.347 117.471 6 AA_U16U17:G84A85_AA A 16 ? A 85 ? A 17 ? A 84 ? 1 A U 17 1_555 A G 84 1_555 A A 18 1_555 A A 6 1_555 5.581 0.494 3.219 118.963 -91.402 -48.205 -0.088 3.088 -2.390 51.032 66.419 -152.688 7 AA_U17A18:A6G84_AA A 17 ? A 84 ? A 18 ? A 6 ? 1 A A 18 1_555 A A 6 1_555 A G 19 1_555 A A 5 1_555 -1.332 -2.940 -1.774 126.943 -116.912 58.808 -1.822 0.288 0.008 -59.734 -64.860 173.535 8 AA_A18G19:A5A6_AA A 18 ? A 6 ? A 19 ? A 5 ? 1 A G 19 1_555 A A 5 1_555 A G 20 1_555 A C 4 1_555 0.680 -1.994 3.300 -2.690 10.054 31.641 -5.012 -1.597 2.502 17.845 4.775 33.267 9 AA_G19G20:C4A5_AA A 19 ? A 5 ? A 20 ? A 4 ? 1 A G 20 1_555 A C 4 1_555 A C 21 1_555 A G 3 1_555 0.846 -1.788 3.093 -0.867 4.769 36.804 -3.388 -1.435 2.828 7.514 1.366 37.111 10 AA_G20C21:G3C4_AA A 20 ? A 4 ? A 21 ? A 3 ? 1 A C 21 1_555 A G 3 1_555 A U 22 1_555 A A 2 1_555 -0.363 -2.079 3.124 1.475 4.992 28.786 -5.091 1.006 2.711 9.939 -2.936 29.243 11 AA_C21U22:A2G3_AA A 21 ? A 3 ? A 22 ? A 2 ? 1 A U 22 1_555 A A 2 1_555 A C 23 1_555 A GTP 1 1_555 1.144 -2.302 3.185 1.430 1.791 27.278 -5.292 -2.078 3.085 3.790 -3.026 27.372 12 AA_U22C23:GTP1A2_AA A 22 ? A 2 ? A 23 ? A 1 ? 1 A C 23 1_555 A GTP 1 1_555 A C 24 1_555 A G 49 1_555 0.080 -2.218 3.100 -2.221 7.287 33.759 -4.718 -0.436 2.570 12.353 3.766 34.583 13 AA_C23C24:G49GTP1_AA A 23 ? A 1 ? A 24 ? A 49 ? 1 A C 24 1_555 A G 49 1_555 A C 25 1_555 A G 48 1_555 -0.463 -1.819 3.009 -5.346 5.865 33.594 -3.874 0.047 2.702 9.975 9.093 34.492 14 AA_C24C25:G48G49_AA A 24 ? A 49 ? A 25 ? A 48 ? 1 A C 25 1_555 A G 48 1_555 A C 26 1_555 A G 47 1_555 -0.508 -1.919 3.478 -1.192 7.730 29.348 -5.209 0.732 2.907 14.926 2.302 30.350 15 AA_C25C26:G47G48_AA A 25 ? A 48 ? A 26 ? A 47 ? 1 A C 26 1_555 A G 47 1_555 A G 27 1_555 A C 46 1_555 -0.421 -1.458 3.398 -2.689 11.856 30.247 -4.598 0.299 2.679 21.654 4.910 32.545 16 AA_C26G27:C46G47_AA A 26 ? A 47 ? A 27 ? A 46 ? 1 A G 27 1_555 A C 46 1_555 A G 28 1_555 A C 45 1_555 0.661 -1.875 3.700 0.605 7.556 30.274 -5.020 -1.107 3.163 14.190 -1.136 31.187 17 AA_G27G28:C45C46_AA A 27 ? A 46 ? A 28 ? A 45 ? 1 A G 28 1_555 A C 45 1_555 A C 29 1_555 A G 44 1_555 -0.094 -1.428 3.041 -0.863 -1.744 37.227 -2.017 0.039 3.104 -2.729 1.351 37.276 18 AA_G28C29:G44C45_AA A 28 ? A 45 ? A 29 ? A 44 ? 1 A C 29 1_555 A G 44 1_555 A G 30 1_555 A U 43 1_555 -0.162 -2.098 2.907 -2.850 16.474 17.891 -8.287 -0.195 0.752 42.746 7.394 24.440 19 AA_C29G30:U43G44_AA A 29 ? A 44 ? A 30 ? A 43 ? 1 A G 30 1_555 A U 43 1_555 A U 31 1_555 A A 42 1_555 -0.019 -1.075 3.338 -4.071 7.602 46.659 -1.951 -0.305 3.127 9.503 5.088 47.406 20 AA_G30U31:A42U43_AA A 30 ? A 43 ? A 31 ? A 42 ? 1 A U 31 1_555 A A 42 1_555 A G 32 1_555 A C 41 1_555 -0.391 -1.725 2.845 1.640 13.089 30.504 -4.702 0.895 1.938 23.543 -2.949 33.172 21 AA_U31G32:C41A42_AA A 31 ? A 42 ? A 32 ? A 41 ? 1 A A 53 1_555 A C 83 1_555 A A 54 1_555 A U 82 1_555 -0.377 -1.068 3.264 -3.083 7.287 44.131 -2.049 0.220 3.077 9.606 4.065 44.799 22 AA_A53A54:U82C83_AA A 53 ? A 83 ? A 54 ? A 82 ? 1 A A 54 1_555 A U 82 1_555 A C 55 1_555 A G 81 1_555 -0.247 -1.434 3.040 2.451 7.130 34.898 -3.254 0.717 2.682 11.720 -4.028 35.679 23 AA_A54C55:G81U82_AA A 54 ? A 82 ? A 55 ? A 81 ? 1 A C 55 1_555 A G 81 1_555 A C 56 1_555 A G 80 1_555 0.470 -1.991 3.611 -1.690 11.617 33.298 -5.018 -1.027 2.757 19.533 2.842 35.252 24 AA_C55C56:G80G81_AA A 55 ? A 81 ? A 56 ? A 80 ? 1 A C 56 1_555 A G 80 1_555 A C 57 1_555 A G 78 1_555 0.813 -1.558 3.247 2.689 6.480 35.404 -3.399 -0.947 2.977 10.528 -4.369 36.071 25 AA_C56C57:G78G80_AA A 56 ? A 80 ? A 57 ? A 78 ? 1 A C 57 1_555 A G 78 1_555 A A 58 1_555 A U 77 1_555 0.213 -1.717 2.885 -4.882 12.442 30.525 -4.621 -1.009 1.996 22.336 8.765 33.259 26 AA_C57A58:U77G78_AA A 57 ? A 78 ? A 58 ? A 77 ? 1 A A 58 1_555 A U 77 1_555 A U 59 1_555 A G 76 1_555 -0.082 -1.380 3.366 1.561 5.559 39.414 -2.670 0.302 3.146 8.188 -2.299 39.818 27 AA_A58U59:G76U77_AA A 58 ? A 77 ? A 59 ? A 76 ? 1 A U 59 1_555 A G 76 1_555 A A 60 1_555 A U 75 1_555 0.071 -1.853 3.103 4.576 10.087 25.962 -5.805 0.761 2.222 21.262 -9.646 28.189 28 AA_U59A60:U75G76_AA A 59 ? A 76 ? A 60 ? A 75 ? 1 A A 60 1_555 A U 75 1_555 A G 61 1_555 A C 74 1_555 -0.333 -1.601 3.325 0.879 8.719 28.183 -4.900 0.831 2.707 17.381 -1.751 29.487 29 AA_A60G61:C74U75_AA A 60 ? A 75 ? A 61 ? A 74 ? 1 A G 61 1_555 A C 74 1_555 A G 62 1_555 A C 73 1_555 0.453 -1.903 3.465 -2.231 9.196 32.019 -4.808 -1.152 2.790 16.234 3.939 33.353 30 AA_G61G62:C73C74_AA A 61 ? A 74 ? A 62 ? A 73 ? 1 A G 62 1_555 A C 73 1_555 A G 63 1_555 A C 72 1_555 0.090 -1.731 3.305 4.046 8.593 31.943 -4.377 0.482 2.750 15.200 -7.156 33.290 31 AA_G62G63:C72C73_AA A 62 ? A 73 ? A 63 ? A 72 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number GM63162-14 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 7-DEAZA-7-AMINOMETHYL-GUANINE PRF 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 4RZD _pdbx_initial_refinement_model.details ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'isothermal titration calorimetry' _pdbx_struct_assembly_auth_evidence.details ? #