data_7KD1 # _entry.id 7KD1 # _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 7KD1 pdb_00007kd1 10.2210/pdb7kd1/pdb WWPDB D_1000252266 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7KD1 _pdbx_database_status.recvd_initial_deposition_date 2020-10-07 _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 'Wilt, H.M.' 1 0000-0001-6983-2700 'Stagno, J.R.' 2 0000-0002-6464-7829 'Wang, Y.-X.' 3 0000-0002-2175-0148 # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Struct.Biol. _citation.journal_id_ASTM JSBIEM _citation.journal_id_CSD 0803 _citation.journal_id_ISSN 1095-8657 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 213 _citation.language ? _citation.page_first 107703 _citation.page_last 107703 _citation.title 'Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation.' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.jsb.2021.107703 _citation.pdbx_database_id_PubMed 33571639 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wilt, H.M.' 1 ? primary 'Yu, P.' 2 ? primary 'Tan, K.' 3 ? primary 'Wang, Y.X.' 4 ? primary 'Stagno, J.R.' 5 ? # _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 7KD1 _cell.details ? _cell.formula_units_Z ? _cell.length_a 74.040 _cell.length_a_esd ? _cell.length_b 74.040 _cell.length_b_esd ? _cell.length_c 122.260 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 6 _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 7KD1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' _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 'tetrahydrofolate riboswitch aptamer domain' 28849.145 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 27 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GGAGAGUAGAUGAUUCGCGUUAAGUGUGUGUGAAUGGGAUGUCGUCACACAACGAAGCGAGAGCGCGGUGAAUCAUUGCA UCCGCUCCA ; _entity_poly.pdbx_seq_one_letter_code_can ;GGAGAGUAGAUGAUUCGCGUUAAGUGUGUGUGAAUGGGAUGUCGUCACACAACGAAGCGAGAGCGCGGUGAAUCAUUGCA UCCGCUCCA ; _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 G n 1 2 G n 1 3 A n 1 4 G n 1 5 A n 1 6 G n 1 7 U n 1 8 A n 1 9 G n 1 10 A n 1 11 U n 1 12 G n 1 13 A n 1 14 U n 1 15 U n 1 16 C n 1 17 G n 1 18 C n 1 19 G n 1 20 U n 1 21 U n 1 22 A n 1 23 A n 1 24 G n 1 25 U n 1 26 G n 1 27 U n 1 28 G n 1 29 U n 1 30 G n 1 31 U n 1 32 G n 1 33 A n 1 34 A n 1 35 U n 1 36 G n 1 37 G n 1 38 G n 1 39 A n 1 40 U n 1 41 G n 1 42 U n 1 43 C n 1 44 G n 1 45 U n 1 46 C n 1 47 A n 1 48 C n 1 49 A n 1 50 C n 1 51 A n 1 52 A n 1 53 C n 1 54 G n 1 55 A n 1 56 A n 1 57 G n 1 58 C n 1 59 G n 1 60 A n 1 61 G n 1 62 A n 1 63 G n 1 64 C n 1 65 G n 1 66 C n 1 67 G n 1 68 G n 1 69 U n 1 70 G n 1 71 A n 1 72 A n 1 73 U n 1 74 C n 1 75 A n 1 76 U n 1 77 U n 1 78 G n 1 79 C n 1 80 A n 1 81 U n 1 82 C n 1 83 C n 1 84 G n 1 85 C n 1 86 U n 1 87 C n 1 88 C n 1 89 A 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 89 _pdbx_entity_src_syn.organism_scientific 'Streptococcus mutans UA159' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 210007 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7KD1 _struct_ref.pdbx_db_accession 7KD1 _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 7KD1 _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 89 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7KD1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 89 _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 89 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 7KD1 _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 3.35 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 63.32 _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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '100 mM MES, pH 5.6, 200 mM NaCl, 2.5 M ammonium sulfate' _exptl_crystal_grow.pdbx_pH_range ? # _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 PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-04-24 _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 0.97930 _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 'APS BEAMLINE 19-ID' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.97930 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 7KD1 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.90 _reflns.d_resolution_low 40.750 _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 30818 _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 98.73 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 7.34 _reflns.pdbx_Rmerge_I_obs 0.026 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 29.4 _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 0.028 _reflns.pdbx_Rpim_I_all 0.010 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 1.000 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.900 _reflns_shell.d_res_low 1.970 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 0.6 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 2962 _reflns_shell.percent_possible_all 97.21 _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 3.639 _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 6.07 _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 3.985 _reflns_shell.pdbx_Rpim_I_all 1.600 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.488 _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 216.860 _refine.B_iso_mean 87.75 _refine.B_iso_min 43.890 _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 7KD1 _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 1.9000 _refine.ls_d_res_low 40.7500 _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 30617 _refine.ls_number_reflns_R_free 1579 _refine.ls_number_reflns_R_work 29038 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.0900 _refine.ls_percent_reflns_R_free 5.1600 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2059 _refine.ls_R_factor_R_free 0.2255 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2048 _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 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 4LVV _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 34.4800 _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 0.3800 _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 1.9000 _refine_hist.d_res_low 40.7500 _refine_hist.number_atoms_solvent 27 _refine_hist.number_atoms_total 1952 _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 89 _refine_hist.pdbx_B_iso_mean_ligand 73.88 _refine_hist.pdbx_B_iso_mean_solvent 63.04 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1914 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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' 1.9000 1.9700 2776 . 142 2634 91.0000 . . . 0.4744 0.0000 0.4494 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 1.9700 2.0500 3021 . 150 2871 98.0000 . . . 0.4516 0.0000 0.4444 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 2.0500 2.1400 3014 . 173 2841 98.0000 . . . 0.4137 0.0000 0.3845 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 2.1400 2.2500 3035 . 129 2906 99.0000 . . . 0.3892 0.0000 0.3410 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 2.2500 2.3900 3080 . 168 2912 99.0000 . . . 0.3138 0.0000 0.3018 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 2.3900 2.5800 3066 . 152 2914 99.0000 . . . 0.3232 0.0000 0.3021 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 2.5800 2.8400 3108 . 147 2961 100.0000 . . . 0.3632 0.0000 0.3163 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 2.8400 3.2500 3110 . 162 2948 99.0000 . . . 0.2892 0.0000 0.2481 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 3.2500 4.0900 3153 . 170 2983 99.0000 . . . 0.1862 0.0000 0.1790 . . . . . . . 10 . . . 'X-RAY DIFFRACTION' 4.0900 40.7500 3254 . 186 3068 98.0000 . . . 0.1749 0.0000 0.1515 . . . . . . . 10 . . . # _struct.entry_id 7KD1 _struct.title 'Apo structure of the THF riboswitch aptamer domain' _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 7KD1 _struct_keywords.text 'riboswitch, apo, gene regulation, 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 2 ? D N N 3 ? E N N 4 ? # 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 metalc1 metalc ? ? A G 1 OP3 ? ? ? 1_555 D MG . MG ? ? A G 1 A MG 103 1_555 ? ? ? ? ? ? ? 2.412 ? ? metalc2 metalc ? ? A G 1 OP1 ? ? ? 1_555 D MG . MG ? ? A G 1 A MG 103 1_555 ? ? ? ? ? ? ? 2.604 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 103 A HOH 223 1_555 ? ? ? ? ? ? ? 2.436 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 88 N3 ? ? A G 1 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 88 O2 ? ? A G 1 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 88 N4 ? ? A G 1 A C 88 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 87 N3 ? ? A G 2 A C 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 87 O2 ? ? A G 2 A C 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 87 N4 ? ? A G 2 A C 87 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 86 N3 ? ? A A 3 A U 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 86 O4 ? ? A A 3 A U 86 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 85 N3 ? ? A G 4 A C 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 85 O2 ? ? A G 4 A C 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 85 N4 ? ? A G 4 A C 85 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A G 84 N1 ? ? A A 5 A G 84 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A G 84 O6 ? ? A A 5 A G 84 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog14 hydrog ? ? A G 6 N2 ? ? ? 1_555 A G 37 O6 ? ? A G 6 A G 37 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog15 hydrog ? ? A A 8 N6 ? ? ? 1_555 A G 78 N3 ? ? A A 8 A G 78 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog16 hydrog ? ? A A 8 N7 ? ? ? 1_555 A G 78 N2 ? ? A A 8 A G 78 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A G 9 N1 ? ? ? 1_555 A U 77 O2 ? ? A G 9 A U 77 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog18 hydrog ? ? A G 9 O6 ? ? ? 1_555 A U 77 N3 ? ? A G 9 A U 77 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog19 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 76 N3 ? ? A A 10 A U 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 76 O4 ? ? A A 10 A U 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 11 N3 ? ? ? 1_555 A A 75 N1 ? ? A U 11 A A 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 11 O4 ? ? ? 1_555 A A 75 N6 ? ? A U 11 A A 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 74 N3 ? ? A G 12 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 74 O2 ? ? A G 12 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 74 N4 ? ? A G 12 A C 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 13 N1 ? ? ? 1_555 A U 73 N3 ? ? A A 13 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 13 N6 ? ? ? 1_555 A U 73 O4 ? ? A A 13 A U 73 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 72 N1 ? ? A U 14 A A 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 72 N6 ? ? A U 14 A A 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 15 N3 ? ? ? 1_555 A A 71 N1 ? ? A U 15 A A 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 15 O4 ? ? ? 1_555 A A 71 N6 ? ? A U 15 A A 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 70 N1 ? ? A C 16 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 70 O6 ? ? A C 16 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 70 N2 ? ? A C 16 A G 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 17 N1 ? ? ? 1_555 A U 69 O2 ? ? A G 17 A U 69 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog36 hydrog ? ? A G 17 O6 ? ? ? 1_555 A U 69 N3 ? ? A G 17 A U 69 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog37 hydrog ? ? A C 18 N3 ? ? ? 1_555 A G 67 N1 ? ? A C 18 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 18 N4 ? ? ? 1_555 A G 67 O6 ? ? A C 18 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 18 O2 ? ? ? 1_555 A G 67 N2 ? ? A C 18 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 19 N2 ? ? ? 1_555 A A 22 N1 ? ? A G 19 A A 22 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog41 hydrog ? ? A G 19 N1 ? ? ? 1_555 A C 66 N3 ? ? A G 19 A C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 19 N2 ? ? ? 1_555 A C 66 O2 ? ? A G 19 A C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 19 O6 ? ? ? 1_555 A C 66 N4 ? ? A G 19 A C 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A U 20 N3 ? ? ? 1_555 A G 65 O6 ? ? A U 20 A G 65 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog45 hydrog ? ? A U 20 O2 ? ? ? 1_555 A G 65 N1 ? ? A U 20 A G 65 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog46 hydrog ? ? A A 23 N6 ? ? ? 1_555 A A 55 N1 ? ? A A 23 A A 55 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog47 hydrog ? ? A A 23 N7 ? ? ? 1_555 A A 55 N6 ? ? A A 23 A A 55 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog48 hydrog ? ? A A 23 N1 ? ? ? 1_555 A G 67 N2 ? ? A A 23 A G 67 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog49 hydrog ? ? A G 24 O6 ? ? ? 1_555 A G 54 N1 ? ? A G 24 A G 54 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog50 hydrog ? ? A U 25 O4 ? ? ? 1_555 A C 53 N4 ? ? A U 25 A C 53 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog51 hydrog ? ? A G 26 N1 ? ? ? 1_555 A A 52 N1 ? ? A G 26 A A 52 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog52 hydrog ? ? A G 26 O6 ? ? ? 1_555 A A 52 N6 ? ? A G 26 A A 52 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog53 hydrog ? ? A U 27 N3 ? ? ? 1_555 A A 51 N1 ? ? A U 27 A A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A U 27 O4 ? ? ? 1_555 A A 51 N6 ? ? A U 27 A A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 28 N1 ? ? ? 1_555 A C 50 N3 ? ? A G 28 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A G 28 N2 ? ? ? 1_555 A C 50 O2 ? ? A G 28 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 28 O6 ? ? ? 1_555 A C 50 N4 ? ? A G 28 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A U 29 N3 ? ? ? 1_555 A A 49 N1 ? ? A U 29 A A 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A U 29 O4 ? ? ? 1_555 A A 49 N6 ? ? A U 29 A A 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A G 30 N1 ? ? ? 1_555 A C 48 N3 ? ? A G 30 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 30 N2 ? ? ? 1_555 A C 48 O2 ? ? A G 30 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A G 30 O6 ? ? ? 1_555 A C 48 N4 ? ? A G 30 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A U 31 N3 ? ? ? 1_555 A A 47 N1 ? ? A U 31 A A 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A U 31 O4 ? ? ? 1_555 A A 47 N6 ? ? A U 31 A A 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A G 32 N1 ? ? ? 1_555 A C 46 N3 ? ? A G 32 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A G 32 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 32 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A G 32 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 32 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A A 33 N1 ? ? ? 1_555 A U 45 N3 ? ? A A 33 A U 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A A 33 N6 ? ? ? 1_555 A U 45 O4 ? ? A A 33 A U 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A U 35 O4 ? ? ? 1_555 A U 42 N3 ? ? A U 35 A U 42 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog71 hydrog ? ? A G 37 N1 ? ? ? 1_555 A C 83 N3 ? ? A G 37 A C 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A G 37 N2 ? ? ? 1_555 A C 83 O2 ? ? A G 37 A C 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A G 37 O6 ? ? ? 1_555 A C 83 N4 ? ? A G 37 A C 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A G 38 N1 ? ? ? 1_555 A C 82 N3 ? ? A G 38 A C 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A G 38 N2 ? ? ? 1_555 A C 82 O2 ? ? A G 38 A C 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A G 38 O6 ? ? ? 1_555 A C 82 N4 ? ? A G 38 A C 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A A 39 N1 ? ? ? 1_555 A U 81 N3 ? ? A A 39 A U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A A 39 N6 ? ? ? 1_555 A U 81 O4 ? ? A A 39 A U 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? A U 40 N3 ? ? ? 1_555 A A 80 N1 ? ? A U 40 A A 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? A U 40 O4 ? ? ? 1_555 A A 80 N6 ? ? A U 40 A A 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? A G 41 N1 ? ? ? 1_555 A C 79 N3 ? ? A G 41 A C 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? A G 41 N2 ? ? ? 1_555 A C 79 O2 ? ? A G 41 A C 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? A G 41 O6 ? ? ? 1_555 A C 79 N4 ? ? A G 41 A C 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? A A 56 N3 ? ? ? 1_555 A G 65 N2 ? ? A A 56 A G 65 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog85 hydrog ? ? A G 57 N1 ? ? ? 1_555 A C 64 N3 ? ? A G 57 A C 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? A G 57 N2 ? ? ? 1_555 A C 64 O2 ? ? A G 57 A C 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? A G 57 O6 ? ? ? 1_555 A C 64 N4 ? ? A G 57 A C 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? A C 58 N3 ? ? ? 1_555 A G 63 N1 ? ? A C 58 A G 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? A C 58 N4 ? ? ? 1_555 A G 63 O6 ? ? A C 58 A G 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? A C 58 O2 ? ? ? 1_555 A G 63 N2 ? ? A C 58 A G 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? A G 59 N2 ? ? ? 1_555 A A 62 N7 ? ? A G 59 A A 62 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _atom_sites.entry_id 7KD1 _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] 0.013506 _atom_sites.fract_transf_matrix[1][2] 0.007798 _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] 0.015596 _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] 0.008179 _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 MG N O P S # 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 A 8 8 8 A A A . n A 1 9 G 9 9 9 G G A . n A 1 10 A 10 10 10 A A A . n A 1 11 U 11 11 11 U U 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 C 16 16 16 C C A . n A 1 17 G 17 17 17 G G A . n A 1 18 C 18 18 18 C C A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 U 21 21 21 U U A . n A 1 22 A 22 22 22 A A A . n A 1 23 A 23 23 23 A A A . n A 1 24 G 24 24 24 G G A . n A 1 25 U 25 25 25 U U A . n A 1 26 G 26 26 26 G G A . n A 1 27 U 27 27 27 U U A . n A 1 28 G 28 28 28 G G A . n A 1 29 U 29 29 29 U U 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 A 33 33 33 A A A . n A 1 34 A 34 34 34 A A A . n A 1 35 U 35 35 35 U U A . n A 1 36 G 36 36 36 G G A . n A 1 37 G 37 37 37 G G A . n A 1 38 G 38 38 38 G G A . n A 1 39 A 39 39 39 A A A . n A 1 40 U 40 40 40 U U A . n A 1 41 G 41 41 41 G G A . n A 1 42 U 42 42 42 U U A . n A 1 43 C 43 43 43 C C A . n A 1 44 G 44 44 44 G G A . n A 1 45 U 45 45 45 U U A . n A 1 46 C 46 46 46 C C A . n A 1 47 A 47 47 47 A A A . n A 1 48 C 48 48 48 C C A . n A 1 49 A 49 49 49 A A A . n A 1 50 C 50 50 50 C C A . n A 1 51 A 51 51 51 A A A . n A 1 52 A 52 52 52 A A A . n A 1 53 C 53 53 53 C C A . n A 1 54 G 54 54 54 G G A . n A 1 55 A 55 55 55 A A A . n A 1 56 A 56 56 56 A A A . n A 1 57 G 57 57 57 G G A . n A 1 58 C 58 58 58 C C A . n A 1 59 G 59 59 59 G G 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 A 62 62 62 A A 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 G 65 65 65 G G A . n A 1 66 C 66 66 66 C C A . n A 1 67 G 67 67 67 G G A . n A 1 68 G 68 68 68 G G A . n A 1 69 U 69 69 69 U U A . n A 1 70 G 70 70 70 G G A . n A 1 71 A 71 71 71 A A A . n A 1 72 A 72 72 72 A A A . n A 1 73 U 73 73 73 U U A . n A 1 74 C 74 74 74 C C A . n A 1 75 A 75 75 75 A A A . n A 1 76 U 76 76 76 U U 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 A 80 80 80 A A A . n A 1 81 U 81 81 81 U U A . n A 1 82 C 82 82 82 C C 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 C 85 85 85 C C A . n A 1 86 U 86 86 86 U U A . n A 1 87 C 87 87 87 C C A . n A 1 88 C 88 88 88 C C A . n A 1 89 A 89 89 89 A A 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 SO4 1 101 1 SO4 SO4 A . C 2 SO4 1 102 2 SO4 SO4 A . D 3 MG 1 103 1 MG MG A . E 4 HOH 1 201 121 HOH HOH A . E 4 HOH 2 202 36 HOH HOH A . E 4 HOH 3 203 123 HOH HOH A . E 4 HOH 4 204 89 HOH HOH A . E 4 HOH 5 205 24 HOH HOH A . E 4 HOH 6 206 100 HOH HOH A . E 4 HOH 7 207 15 HOH HOH A . E 4 HOH 8 208 300 HOH HOH A . E 4 HOH 9 209 16 HOH HOH A . E 4 HOH 10 210 110 HOH HOH A . E 4 HOH 11 211 113 HOH HOH A . E 4 HOH 12 212 90 HOH HOH A . E 4 HOH 13 213 92 HOH HOH A . E 4 HOH 14 214 49 HOH HOH A . E 4 HOH 15 215 117 HOH HOH A . E 4 HOH 16 216 120 HOH HOH A . E 4 HOH 17 217 122 HOH HOH A . E 4 HOH 18 218 119 HOH HOH A . E 4 HOH 19 219 81 HOH HOH A . E 4 HOH 20 220 298 HOH HOH A . E 4 HOH 21 221 118 HOH HOH A . E 4 HOH 22 222 27 HOH HOH A . E 4 HOH 23 223 80 HOH HOH A . E 4 HOH 24 224 296 HOH HOH A . E 4 HOH 25 225 297 HOH HOH A . E 4 HOH 26 226 79 HOH HOH A . E 4 HOH 27 227 74 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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,D,E # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 206 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id E _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP3 ? A G 1 ? A G 1 ? 1_555 MG ? D MG . ? A MG 103 ? 1_555 OP1 ? A G 1 ? A G 1 ? 1_555 57.3 ? 2 OP3 ? A G 1 ? A G 1 ? 1_555 MG ? D MG . ? A MG 103 ? 1_555 O ? E HOH . ? A HOH 223 ? 1_555 87.7 ? 3 OP1 ? A G 1 ? A G 1 ? 1_555 MG ? D MG . ? A MG 103 ? 1_555 O ? E HOH . ? A HOH 223 ? 1_555 74.0 ? # 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 2021-03-03 2 'Structure model' 1 1 2021-03-10 3 'Structure model' 1 2 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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' citation 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.title' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' # 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 22.8297 42.7088 92.0426 1.1142 ? 0.2094 ? 0.0281 ? 0.7494 ? -0.1211 ? 0.8254 ? 0.3146 ? -1.1628 ? -0.9468 ? 1.4660 ? 3.2790 ? 1.4988 ? -0.2232 ? -0.1883 ? 0.2524 ? 0.7269 ? 0.2734 ? -0.1954 ? 0.5419 ? 0.3143 ? -0.1835 ? 2 'X-RAY DIFFRACTION' ? refined 18.2042 21.6833 77.6655 0.7155 ? 0.0337 ? 0.0446 ? 0.5828 ? 0.0741 ? 0.6432 ? 1.1938 ? 0.6881 ? -0.1384 ? 2.4408 ? -1.5989 ? 2.1659 ? -0.0939 ? -0.1578 ? -0.3739 ? -0.0042 ? 0.1575 ? -0.2057 ? 0.4561 ? -0.2933 ? -0.0252 ? 3 'X-RAY DIFFRACTION' ? refined 12.0471 30.3639 104.7161 1.9285 ? 0.3465 ? 0.2943 ? 1.0171 ? -0.1064 ? 1.0114 ? 0.0588 ? -0.7242 ? -0.5864 ? 3.8850 ? 2.6985 ? 1.6736 ? 0.4514 ? -0.2528 ? 0.6278 ? 1.5118 ? -0.5261 ? 0.9246 ? -0.6164 ? -0.9114 ? 0.0226 ? 4 'X-RAY DIFFRACTION' ? refined 24.1222 27.7263 70.1689 0.5835 ? 0.0667 ? 0.0215 ? 0.5872 ? -0.0069 ? 0.5672 ? 0.0104 ? -0.0524 ? -0.3430 ? 0.8233 ? -0.5778 ? 2.0088 ? 0.0058 ? 0.0880 ? -0.0934 ? 0.0449 ? 0.1931 ? -0.1164 ? 0.3308 ? 0.0865 ? -0.1240 ? 5 'X-RAY DIFFRACTION' ? refined 19.5328 43.5590 98.1088 1.2310 ? 0.2548 ? -0.0029 ? 0.9091 ? -0.1703 ? 0.7494 ? -0.6074 ? -0.1154 ? -0.3816 ? 1.0337 ? 3.5974 ? 3.0085 ? -0.1629 ? -0.1620 ? 0.2179 ? 0.5745 ? 0.0559 ? -0.0773 ? 0.2647 ? -0.1262 ? -0.1185 ? # 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 1 ? ? ? A 20 ? ? ;chain 'A' and (resid 1 through 20 ) ; 2 'X-RAY DIFFRACTION' 2 ? ? A 21 ? ? ? A 30 ? ? ;chain 'A' and (resid 21 through 30 ) ; 3 'X-RAY DIFFRACTION' 3 ? ? A 31 ? ? ? A 45 ? ? ;chain 'A' and (resid 31 through 45 ) ; 4 'X-RAY DIFFRACTION' 4 ? ? A 46 ? ? ? A 65 ? ? ;chain 'A' and (resid 46 through 65 ) ; 5 'X-RAY DIFFRACTION' 5 ? ? A 66 ? ? ? A 89 ? ? ;chain 'A' and (resid 66 through 89 ) ; # 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 ? ? ? dev-3900 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? 20200131 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? 20200131 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _pdbx_entry_details.entry_id 7KD1 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P A G 1 ? ? OP3 A G 1 ? ? 1.471 1.607 -0.136 0.012 N 2 1 N9 A A 56 ? ? C4 A A 56 ? ? 1.335 1.374 -0.039 0.006 N 3 1 P A G 67 ? ? OP1 A G 67 ? ? 1.363 1.485 -0.122 0.017 N # 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 "O4'" A A 22 ? ? "C1'" A A 22 ? ? N9 A A 22 ? ? 112.86 108.50 4.36 0.70 N 2 1 "O5'" A A 23 ? ? P A A 23 ? ? OP2 A A 23 ? ? 99.39 105.70 -6.31 0.90 N 3 1 C5 A G 24 ? ? C6 A G 24 ? ? O6 A G 24 ? ? 124.76 128.60 -3.84 0.60 N 4 1 C4 A G 30 ? ? C5 A G 30 ? ? N7 A G 30 ? ? 113.33 110.80 2.53 0.40 N 5 1 C6 A C 43 ? ? N1 A C 43 ? ? C2 A C 43 ? ? 116.91 120.30 -3.39 0.40 N 6 1 N3 A G 44 ? ? C4 A G 44 ? ? C5 A G 44 ? ? 125.59 128.60 -3.01 0.50 N 7 1 N3 A G 44 ? ? C4 A G 44 ? ? N9 A G 44 ? ? 129.95 126.00 3.95 0.60 N 8 1 C8 A G 44 ? ? N9 A G 44 ? ? "C1'" A G 44 ? ? 118.91 127.00 -8.09 1.30 N 9 1 C4 A G 44 ? ? N9 A G 44 ? ? "C1'" A G 44 ? ? 136.11 126.50 9.61 1.30 N 10 1 C6 A C 46 ? ? N1 A C 46 ? ? C2 A C 46 ? ? 117.61 120.30 -2.69 0.40 N 11 1 "O5'" A A 49 ? ? P A A 49 ? ? OP2 A A 49 ? ? 99.43 105.70 -6.27 0.90 N 12 1 "O4'" A A 55 ? ? "C1'" A A 55 ? ? N9 A A 55 ? ? 113.50 108.50 5.00 0.70 N 13 1 C5 A G 59 ? ? C6 A G 59 ? ? O6 A G 59 ? ? 124.87 128.60 -3.73 0.60 N 14 1 N7 A G 61 ? ? C8 A G 61 ? ? N9 A G 61 ? ? 109.84 113.10 -3.26 0.50 N 15 1 C8 A G 61 ? ? N9 A G 61 ? ? C4 A G 61 ? ? 108.81 106.40 2.41 0.40 N 16 1 C8 A G 65 ? ? N9 A G 65 ? ? C4 A G 65 ? ? 109.10 106.40 2.70 0.40 N 17 1 "O5'" A C 66 ? ? P A C 66 ? ? OP1 A C 66 ? ? 117.94 110.70 7.24 1.20 N 18 1 C5 A G 70 ? ? N7 A G 70 ? ? C8 A G 70 ? ? 101.08 104.30 -3.22 0.50 N 19 1 "O5'" A A 71 ? ? P A A 71 ? ? OP1 A A 71 ? ? 118.45 110.70 7.75 1.20 N # 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 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 MG MG MG N N 114 SO4 S S N N 115 SO4 O1 O N N 116 SO4 O2 O N N 117 SO4 O3 O N N 118 SO4 O4 O N N 119 U OP3 O N N 120 U P P N N 121 U OP1 O N N 122 U OP2 O N N 123 U "O5'" O N N 124 U "C5'" C N N 125 U "C4'" C N R 126 U "O4'" O N N 127 U "C3'" C N S 128 U "O3'" O N N 129 U "C2'" C N R 130 U "O2'" O N N 131 U "C1'" C N R 132 U N1 N N N 133 U C2 C N N 134 U O2 O N N 135 U N3 N N N 136 U C4 C N N 137 U O4 O N N 138 U C5 C N N 139 U C6 C N N 140 U HOP3 H N N 141 U HOP2 H N N 142 U "H5'" H N N 143 U "H5''" H N N 144 U "H4'" H N N 145 U "H3'" H N N 146 U "HO3'" H N N 147 U "H2'" H N N 148 U "HO2'" H N N 149 U "H1'" H N N 150 U H3 H N N 151 U H5 H N N 152 U H6 H N N 153 # 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 HOH O H1 sing N N 116 HOH O H2 sing N N 117 SO4 S O1 doub N N 118 SO4 S O2 doub N N 119 SO4 S O3 sing N N 120 SO4 S O4 sing N N 121 U OP3 P sing N N 122 U OP3 HOP3 sing N N 123 U P OP1 doub N N 124 U P OP2 sing N N 125 U P "O5'" sing N N 126 U OP2 HOP2 sing N N 127 U "O5'" "C5'" sing N N 128 U "C5'" "C4'" sing N N 129 U "C5'" "H5'" sing N N 130 U "C5'" "H5''" sing N N 131 U "C4'" "O4'" sing N N 132 U "C4'" "C3'" sing N N 133 U "C4'" "H4'" sing N N 134 U "O4'" "C1'" sing N N 135 U "C3'" "O3'" sing N N 136 U "C3'" "C2'" sing N N 137 U "C3'" "H3'" sing N N 138 U "O3'" "HO3'" sing N N 139 U "C2'" "O2'" sing N N 140 U "C2'" "C1'" sing N N 141 U "C2'" "H2'" sing N N 142 U "O2'" "HO2'" sing N N 143 U "C1'" N1 sing N N 144 U "C1'" "H1'" sing N N 145 U N1 C2 sing N N 146 U N1 C6 sing N N 147 U C2 O2 doub N N 148 U C2 N3 sing N N 149 U N3 C4 sing N N 150 U N3 H3 sing N N 151 U C4 O4 doub N N 152 U C4 C5 sing N N 153 U C5 C6 doub N N 154 U C5 H5 sing N N 155 U C6 H6 sing N N 156 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7KD1 'double helix' 7KD1 'a-form double helix' 7KD1 'bulge loop' 7KD1 'mismatched base pair' 7KD1 '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 1 1_555 A C 88 1_555 -0.114 -0.267 0.158 1.204 1.406 -4.013 1 A_G1:C88_A A 1 ? A 88 ? 19 1 1 A G 2 1_555 A C 87 1_555 -0.270 -0.226 0.032 -1.624 -15.596 1.261 2 A_G2:C87_A A 2 ? A 87 ? 19 1 1 A A 3 1_555 A U 86 1_555 0.125 -0.184 0.304 -2.663 -10.064 3.720 3 A_A3:U86_A A 3 ? A 86 ? 20 1 1 A G 4 1_555 A C 85 1_555 -0.339 -0.119 0.066 -13.197 -19.235 -0.650 4 A_G4:C85_A A 4 ? A 85 ? 19 1 1 A A 5 1_555 A G 84 1_555 -0.032 1.590 -0.072 -24.066 -8.750 -17.995 5 A_A5:G84_A A 5 ? A 84 ? 8 1 1 A G 37 1_555 A C 83 1_555 -0.239 -0.062 -0.404 -1.608 0.042 0.446 6 A_G37:C83_A A 37 ? A 83 ? 19 1 1 A G 38 1_555 A C 82 1_555 -0.310 -0.129 -0.208 -6.564 -5.362 2.721 7 A_G38:C82_A A 38 ? A 82 ? 19 1 1 A A 39 1_555 A U 81 1_555 0.183 -0.068 -0.201 -4.832 1.531 -0.743 8 A_A39:U81_A A 39 ? A 81 ? 20 1 1 A U 40 1_555 A A 80 1_555 0.085 -0.056 -0.273 0.756 2.655 0.571 9 A_U40:A80_A A 40 ? A 80 ? 20 1 1 A G 41 1_555 A C 79 1_555 -0.295 0.057 0.350 0.468 -9.657 6.597 10 A_G41:C79_A A 41 ? A 79 ? 19 1 1 A U 42 1_555 A U 35 1_555 3.678 -0.886 1.437 12.064 20.375 -95.281 11 A_U42:U35_A A 42 ? A 35 ? ? 4 1 A A 8 1_555 A G 78 1_555 -6.698 -4.686 0.128 0.719 -11.926 -1.812 12 A_A8:G78_A A 8 ? A 78 ? 11 10 1 A G 9 1_555 A U 77 1_555 -2.099 -0.559 -0.059 4.600 -8.654 1.407 13 A_G9:U77_A A 9 ? A 77 ? 28 1 1 A A 10 1_555 A U 76 1_555 -0.094 -0.114 0.270 1.025 -14.075 3.500 14 A_A10:U76_A A 10 ? A 76 ? 20 1 1 A U 11 1_555 A A 75 1_555 -0.025 -0.092 0.258 -0.882 -11.523 3.246 15 A_U11:A75_A A 11 ? A 75 ? 20 1 1 A G 12 1_555 A C 74 1_555 -0.238 -0.190 0.084 -2.391 -9.426 0.053 16 A_G12:C74_A A 12 ? A 74 ? 19 1 1 A A 13 1_555 A U 73 1_555 0.150 -0.183 0.124 -3.137 -11.339 0.423 17 A_A13:U73_A A 13 ? A 73 ? 20 1 1 A U 14 1_555 A A 72 1_555 0.036 -0.050 0.159 -5.863 -11.612 2.013 18 A_U14:A72_A A 14 ? A 72 ? 20 1 1 A U 15 1_555 A A 71 1_555 -0.206 -0.091 0.227 -3.456 -10.824 1.119 19 A_U15:A71_A A 15 ? A 71 ? 20 1 1 A C 16 1_555 A G 70 1_555 0.157 -0.246 0.312 -1.115 -5.156 -3.613 20 A_C16:G70_A A 16 ? A 70 ? 19 1 1 A G 17 1_555 A U 69 1_555 -2.241 -0.694 -0.128 -0.915 -10.075 -1.492 21 A_G17:U69_A A 17 ? A 69 ? 28 1 1 A C 18 1_555 A G 67 1_555 0.204 -0.144 -0.082 6.259 -11.118 1.305 22 A_C18:G67_A A 18 ? A 67 ? 19 1 1 A G 19 1_555 A C 66 1_555 -0.316 -0.074 0.001 -1.034 -21.763 2.935 23 A_G19:C66_A A 19 ? A 66 ? 19 1 1 A U 20 1_555 A G 65 1_555 2.253 -0.460 0.051 -5.256 -15.890 -4.403 24 A_U20:G65_A A 20 ? A 65 ? 28 1 1 A G 57 1_555 A C 64 1_555 -0.146 -0.075 -0.097 -12.749 -4.090 1.212 25 A_G57:C64_A A 57 ? A 64 ? 19 1 1 A C 58 1_555 A G 63 1_555 0.209 -0.133 0.099 -1.623 -0.184 -2.526 26 A_C58:G63_A A 58 ? A 63 ? 19 1 1 A G 59 1_555 A A 62 1_555 7.140 -4.934 0.766 6.643 -8.867 -18.253 27 A_G59:A62_A A 59 ? A 62 ? ? ? 1 A A 23 1_555 A A 55 1_555 -4.069 1.524 -0.372 -10.865 -4.780 -112.715 28 A_A23:A55_A A 23 ? A 55 ? 5 4 1 A G 24 1_555 A G 54 1_555 -3.964 1.171 0.079 9.037 -12.631 -64.101 29 A_G24:G54_A A 24 ? A 54 ? ? 1 1 A U 25 1_555 A C 53 1_555 -0.651 2.072 -1.347 5.907 -25.198 -69.566 30 A_U25:C53_A A 25 ? A 53 ? ? ? 1 A G 26 1_555 A A 52 1_555 -0.060 1.402 -0.447 1.671 -20.244 -17.662 31 A_G26:A52_A A 26 ? A 52 ? 8 1 1 A U 27 1_555 A A 51 1_555 -0.033 -0.135 0.019 8.929 -17.863 -3.669 32 A_U27:A51_A A 27 ? A 51 ? 20 1 1 A G 28 1_555 A C 50 1_555 -0.189 -0.217 0.016 -1.618 -15.135 -0.027 33 A_G28:C50_A A 28 ? A 50 ? 19 1 1 A U 29 1_555 A A 49 1_555 -0.043 -0.166 0.177 0.013 -12.942 2.197 34 A_U29:A49_A A 29 ? A 49 ? 20 1 1 A G 30 1_555 A C 48 1_555 -0.313 -0.240 0.117 -7.239 -13.959 -0.146 35 A_G30:C48_A A 30 ? A 48 ? 19 1 1 A U 31 1_555 A A 47 1_555 -0.033 -0.182 0.233 -7.982 -10.905 1.477 36 A_U31:A47_A A 31 ? A 47 ? 20 1 1 A G 32 1_555 A C 46 1_555 -0.087 -0.112 -0.039 -8.868 -13.157 -2.841 37 A_G32:C46_A A 32 ? A 46 ? 19 1 1 A A 33 1_555 A U 45 1_555 0.067 -0.243 0.693 6.108 -9.755 -3.053 38 A_A33:U45_A A 33 ? A 45 ? 20 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 1 1_555 A C 88 1_555 A G 2 1_555 A C 87 1_555 0.636 -2.232 3.221 0.988 10.018 33.648 -5.044 -0.924 2.492 16.843 -1.661 35.080 1 AA_G1G2:C87C88_AA A 1 ? A 88 ? A 2 ? A 87 ? 1 A G 2 1_555 A C 87 1_555 A A 3 1_555 A U 86 1_555 0.368 -1.759 3.219 0.346 1.467 32.049 -3.440 -0.605 3.142 2.656 -0.626 32.084 2 AA_G2A3:U86C87_AA A 2 ? A 87 ? A 3 ? A 86 ? 1 A A 3 1_555 A U 86 1_555 A G 4 1_555 A C 85 1_555 0.650 -2.267 3.400 7.360 8.358 31.748 -5.259 0.052 2.807 14.724 -12.966 33.597 3 AA_A3G4:C85U86_AA A 3 ? A 86 ? A 4 ? A 85 ? 1 A G 4 1_555 A C 85 1_555 A A 5 1_555 A G 84 1_555 -1.103 -1.926 3.211 2.537 4.780 36.272 -3.673 2.078 2.862 7.626 -4.048 36.660 4 AA_G4A5:G84C85_AA A 4 ? A 85 ? A 5 ? A 84 ? 1 A A 5 1_555 A G 84 1_555 A G 37 1_555 A C 83 1_555 -2.122 -3.289 3.332 18.878 2.157 49.471 -3.825 3.481 2.299 2.475 -21.658 52.780 5 AA_A5G37:C83G84_AA A 5 ? A 84 ? A 37 ? A 83 ? 1 A G 37 1_555 A C 83 1_555 A G 38 1_555 A C 82 1_555 -0.647 -2.538 3.529 -3.211 0.454 29.066 -5.135 0.528 3.539 0.901 6.372 29.242 6 AA_G37G38:C82C83_AA A 37 ? A 83 ? A 38 ? A 82 ? 1 A G 38 1_555 A C 82 1_555 A A 39 1_555 A U 81 1_555 -0.898 -2.107 3.081 -2.274 9.145 28.674 -5.645 1.330 2.374 17.866 4.443 30.152 7 AA_G38A39:U81C82_AA A 38 ? A 82 ? A 39 ? A 81 ? 1 A A 39 1_555 A U 81 1_555 A U 40 1_555 A A 80 1_555 0.130 -1.335 3.302 0.690 7.308 28.635 -4.109 -0.115 2.882 14.477 -1.366 29.541 8 AA_A39U40:A80U81_AA A 39 ? A 81 ? A 40 ? A 80 ? 1 A U 40 1_555 A A 80 1_555 A G 41 1_555 A C 79 1_555 1.129 -1.539 3.068 0.569 12.233 32.022 -4.271 -1.841 2.359 21.229 -0.988 34.226 9 AA_U40G41:C79A80_AA A 40 ? A 80 ? A 41 ? A 79 ? 1 A G 41 1_555 A C 79 1_555 A U 42 1_555 A U 35 1_555 -2.844 -2.865 3.337 8.982 18.119 70.576 -2.927 2.647 2.317 15.371 -7.619 73.053 10 AA_G41U42:U35C79_AA A 41 ? A 79 ? A 42 ? A 35 ? 1 A A 8 1_555 A G 78 1_555 A G 9 1_555 A U 77 1_555 1.231 -0.853 3.269 -4.226 6.844 54.770 -1.309 -1.568 3.055 7.394 4.566 55.313 11 AA_A8G9:U77G78_AA A 8 ? A 78 ? A 9 ? A 77 ? 1 A G 9 1_555 A U 77 1_555 A A 10 1_555 A U 76 1_555 -0.328 -1.689 3.323 -4.549 2.038 39.142 -2.744 -0.055 3.251 3.027 6.756 39.446 12 AA_G9A10:U76U77_AA A 9 ? A 77 ? A 10 ? A 76 ? 1 A A 10 1_555 A U 76 1_555 A U 11 1_555 A A 75 1_555 -0.386 -1.462 3.297 -1.199 0.988 31.483 -2.876 0.487 3.263 1.819 2.207 31.521 13 AA_A10U11:A75U76_AA A 10 ? A 76 ? A 11 ? A 75 ? 1 A U 11 1_555 A A 75 1_555 A G 12 1_555 A C 74 1_555 -0.214 -1.580 3.095 0.476 9.044 31.031 -4.252 0.460 2.543 16.469 -0.866 32.295 14 AA_U11G12:C74A75_AA A 11 ? A 75 ? A 12 ? A 74 ? 1 A G 12 1_555 A C 74 1_555 A A 13 1_555 A U 73 1_555 -0.164 -1.020 3.212 -1.855 6.985 35.754 -2.556 0.016 2.971 11.235 2.984 36.453 15 AA_G12A13:U73C74_AA A 12 ? A 74 ? A 13 ? A 73 ? 1 A A 13 1_555 A U 73 1_555 A U 14 1_555 A A 72 1_555 -0.013 -1.091 3.262 0.590 9.449 32.330 -3.353 0.113 2.838 16.531 -1.032 33.653 16 AA_A13U14:A72U73_AA A 13 ? A 73 ? A 14 ? A 72 ? 1 A U 14 1_555 A A 72 1_555 A U 15 1_555 A A 71 1_555 0.033 -0.969 3.157 0.036 6.309 32.603 -2.689 -0.053 2.923 11.109 -0.063 33.191 17 AA_U14U15:A71A72_AA A 14 ? A 72 ? A 15 ? A 71 ? 1 A U 15 1_555 A A 71 1_555 A C 16 1_555 A G 70 1_555 0.108 -1.214 3.193 -0.781 2.799 32.723 -2.608 -0.320 3.078 4.957 1.384 32.848 18 AA_U15C16:G70A71_AA A 15 ? A 71 ? A 16 ? A 70 ? 1 A C 16 1_555 A G 70 1_555 A G 17 1_555 A U 69 1_555 1.658 -2.443 3.212 3.385 5.207 22.215 -7.817 -3.040 2.792 13.186 -8.573 23.056 19 AA_C16G17:U69G70_AA A 16 ? A 70 ? A 17 ? A 69 ? 1 A G 17 1_555 A U 69 1_555 A C 18 1_555 A G 67 1_555 -0.064 -1.576 3.150 -3.037 -1.251 44.191 -1.977 -0.189 3.188 -1.661 4.030 44.307 20 AA_G17C18:G67U69_AA A 17 ? A 69 ? A 18 ? A 67 ? 1 A C 18 1_555 A G 67 1_555 A G 19 1_555 A C 66 1_555 -0.156 -1.436 3.335 -3.185 17.134 32.093 -4.493 -0.158 2.307 28.519 5.302 36.410 21 AA_C18G19:C66G67_AA A 18 ? A 67 ? A 19 ? A 66 ? 1 A G 19 1_555 A C 66 1_555 A U 20 1_555 A G 65 1_555 0.003 -1.135 3.284 1.122 2.556 44.780 -1.718 0.098 3.217 3.351 -1.471 44.862 22 AA_G19U20:G65C66_AA A 19 ? A 66 ? A 20 ? A 65 ? 1 A U 20 1_555 A G 65 1_555 A G 57 1_555 A C 64 1_555 -1.857 -2.149 3.255 3.232 9.758 34.134 -4.767 3.452 2.390 16.174 -5.357 35.604 23 AA_U20G57:C64G65_AA A 20 ? A 65 ? A 57 ? A 64 ? 1 A G 57 1_555 A C 64 1_555 A C 58 1_555 A G 63 1_555 -0.415 -1.462 3.135 -1.677 1.837 31.990 -2.959 0.466 3.065 3.326 3.037 32.084 24 AA_G57C58:G63C64_AA A 57 ? A 64 ? A 58 ? A 63 ? 1 A C 58 1_555 A G 63 1_555 A G 59 1_555 A A 62 1_555 -2.126 -1.005 3.023 -1.546 7.052 49.493 -1.657 2.413 2.924 8.371 1.836 49.984 25 AA_C58G59:A62G63_AA A 58 ? A 63 ? A 59 ? A 62 ? 1 A A 23 1_555 A A 55 1_555 A G 24 1_555 A G 54 1_555 2.425 -2.149 2.888 -6.455 2.070 35.275 -3.724 -4.673 2.297 3.378 10.531 35.900 26 AA_A23G24:G54A55_AA A 23 ? A 55 ? A 24 ? A 54 ? 1 A G 24 1_555 A G 54 1_555 A U 25 1_555 A C 53 1_555 -0.291 -2.969 3.721 -2.475 14.451 47.098 -4.666 0.161 2.762 17.592 3.013 49.203 27 AA_G24U25:C53G54_AA A 24 ? A 54 ? A 25 ? A 53 ? 1 A U 25 1_555 A C 53 1_555 A G 26 1_555 A A 52 1_555 2.230 -2.027 3.237 -2.220 5.217 34.421 -4.113 -4.032 2.765 8.742 3.721 34.871 28 AA_U25G26:A52C53_AA A 25 ? A 53 ? A 26 ? A 52 ? 1 A G 26 1_555 A A 52 1_555 A U 27 1_555 A A 51 1_555 0.969 -0.796 3.045 -4.730 1.845 32.908 -1.668 -2.405 2.834 3.233 8.288 33.287 29 AA_G26U27:A51A52_AA A 26 ? A 52 ? A 27 ? A 51 ? 1 A U 27 1_555 A A 51 1_555 A G 28 1_555 A C 50 1_555 0.183 -1.630 3.360 -2.849 13.770 33.185 -4.471 -0.675 2.488 22.875 4.733 35.964 30 AA_U27G28:C50A51_AA A 27 ? A 51 ? A 28 ? A 50 ? 1 A G 28 1_555 A C 50 1_555 A U 29 1_555 A A 49 1_555 0.103 -1.407 3.138 -2.065 4.314 34.526 -2.961 -0.464 2.935 7.225 3.458 34.846 31 AA_G28U29:A49C50_AA A 28 ? A 50 ? A 29 ? A 49 ? 1 A U 29 1_555 A A 49 1_555 A G 30 1_555 A C 48 1_555 -0.300 -1.748 3.245 0.266 13.978 30.771 -5.016 0.556 2.259 24.798 -0.472 33.728 32 AA_U29G30:C48A49_AA A 29 ? A 49 ? A 30 ? A 48 ? 1 A G 30 1_555 A C 48 1_555 A U 31 1_555 A A 47 1_555 0.689 -1.372 3.239 0.522 4.337 31.611 -3.256 -1.163 3.039 7.915 -0.952 31.904 33 AA_G30U31:A47C48_AA A 30 ? A 48 ? A 31 ? A 47 ? 1 A U 31 1_555 A A 47 1_555 A G 32 1_555 A C 46 1_555 -0.062 -1.625 3.292 3.673 4.108 30.704 -3.784 0.797 3.027 7.681 -6.867 31.183 34 AA_U31G32:C46A47_AA A 31 ? A 47 ? A 32 ? A 46 ? 1 A G 32 1_555 A C 46 1_555 A A 33 1_555 A U 45 1_555 0.504 -1.154 2.868 -3.504 -5.167 33.987 -1.228 -1.335 2.942 -8.748 5.933 34.539 35 AA_G32A33:U45C46_AA A 32 ? A 46 ? A 33 ? A 45 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 'MAGNESIUM ION' MG 4 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 4LVV _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 'native gel electrophoresis' _pdbx_struct_assembly_auth_evidence.details ? #