data_5UX3 # _entry.id 5UX3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 5UX3 pdb_00005ux3 10.2210/pdb5ux3/pdb WWPDB D_1000226544 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5UX3 _pdbx_database_status.recvd_initial_deposition_date 2017-02-21 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Zhang, W.' 1 ? 'Oh, S.S.' 2 ? 'Szostak, J.W.' 3 ? # _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. Am. Chem. Soc.' _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 140 _citation.language ? _citation.page_first 2829 _citation.page_last 2840 _citation.title 'Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.7b11750 _citation.pdbx_database_id_PubMed 29411978 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, W.' 1 ? primary 'Tam, C.P.' 2 ? primary 'Zhou, L.' 3 ? primary 'Oh, S.S.' 4 ? primary 'Wang, J.' 5 ? primary 'Szostak, J.W.' 6 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5UX3 _cell.details ? _cell.formula_units_Z ? _cell.length_a 46.527 _cell.length_a_esd ? _cell.length_b 46.527 _cell.length_b_esd ? _cell.length_c 156.938 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _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 5UX3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 'RNA (25-MER)' 8238.869 1 ? ? ? ? 2 polymer syn ;RNA (5'-D(*(RG))-R(P*CP*AP*CP*CP*UP*CP*A)-3') ; 2549.641 1 ? ? ? ? 3 non-polymer syn "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" 427.309 1 ? ? ? ? 4 water nat water 18.015 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no yes 'UGAGG(5BU)G(LCC)(LCC)GAGCGCGAAAGCGCUC' UGAGGUGNNGAGCGCGAAAGCGCUC A ? 2 polyribonucleotide no yes '(8OS)CACCUCA' XCACCUCA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 A n 1 4 G n 1 5 G n 1 6 5BU n 1 7 G n 1 8 LCC n 1 9 LCC n 1 10 G n 1 11 A n 1 12 G n 1 13 C n 1 14 G n 1 15 C n 1 16 G n 1 17 A n 1 18 A n 1 19 A n 1 20 G n 1 21 C n 1 22 G n 1 23 C n 1 24 U n 1 25 C n 2 1 8OS n 2 2 C n 2 3 A n 2 4 C n 2 5 C n 2 6 U n 2 7 C n 2 8 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 25 'synthetic construct' ? 32630 ? 2 1 sample 1 8 'synthetic construct' ? 32630 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5UX3 5UX3 ? 1 ? 1 2 PDB 5UX3 5UX3 ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5UX3 A 1 ? 25 ? 5UX3 1 ? 25 ? 1 25 2 2 5UX3 B 1 ? 8 ? 5UX3 1 ? 8 ? 1 8 # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 8OS 'RNA linking' n "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" ? 'C14 H18 N7 O7 P' 427.309 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 LCC 'RNA linking' . '[(1R,3R,4R,7S)-7-HYDROXY-3-(5-METHYLCYTOSIN-1-YL)-2,5-DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE' ? 'C11 H16 N3 O8 P' 349.234 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 5UX3 _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 3.8 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 68.1 _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 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 99 _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_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-10-28 # _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 1 _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 'ALS BEAMLINE 8.2.2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_synchrotron_site ALS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5UX3 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.50 _reflns.d_resolution_low 50 _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 6436 _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 98.7 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.1 _reflns.pdbx_Rmerge_I_obs 0.080 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value 0.067 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 20.3 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.02 _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 ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.943 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.59 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 604 _reflns_shell.percent_possible_all 94.1 _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 0.695 _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 3.9 _reflns_shell.pdbx_Rsym_value 0.463 _reflns_shell.pdbx_chi_squared 0.639 _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 ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.754 _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] -0.07 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][2] -0.07 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] 0.15 _refine.B_iso_max ? _refine.B_iso_mean 77.743 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.893 _refine.correlation_coeff_Fo_to_Fc_free 0.957 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 5UX3 _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 2.50 _refine.ls_d_res_low 44.61 _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 6154 _refine.ls_number_reflns_R_free 281 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.74 _refine.ls_percent_reflns_R_free 4.4 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.22040 _refine.ls_R_factor_R_free 0.26127 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.21848 _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 ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _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 ? _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 4FNJ _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.270 _refine.pdbx_overall_ESU_R_Free 0.232 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _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 ? _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 13.705 _refine.overall_SU_ML 0.260 _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 1 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 714 _refine_hist.pdbx_number_atoms_ligand 29 _refine_hist.number_atoms_solvent 1 _refine_hist.number_atoms_total 744 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 44.61 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.015 0.013 826 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.013 0.022 355 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 2.564 1.552 1275 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 2.791 3.108 852 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.252 0.200 141 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.012 0.020 433 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.003 0.020 185 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 7.000 8.246 826 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 6.997 8.248 827 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 9.462 12.321 1276 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 10.276 84.278 1203 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 10.275 84.290 1204 ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 2.501 _refine_ls_shell.d_res_low 2.566 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 18 _refine_ls_shell.number_reflns_R_work 423 _refine_ls_shell.percent_reflns_obs 94.43 _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 0.598 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.476 _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_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5UX3 _struct.title 'RNA hairpin structure containing 2-MeImpG monomer analogue and 2-MeImp-oligomer analogue' _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 5UX3 _struct_keywords.text 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 ? D 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 covale1 covale both ? A G 5 "O3'" ? ? ? 1_555 A 5BU 6 P ? ? A G 5 A 5BU 6 1_555 ? ? ? ? ? ? ? 1.674 ? ? covale2 covale both ? A 5BU 6 "O3'" ? ? ? 1_555 A G 7 P ? ? A 5BU 6 A G 7 1_555 ? ? ? ? ? ? ? 1.705 ? ? covale3 covale both ? A G 7 "O3'" ? ? ? 1_555 A LCC 8 P ? ? A G 7 A LCC 8 1_555 ? ? ? ? ? ? ? 1.626 ? ? covale4 covale both ? A LCC 8 "O3'" ? ? ? 1_555 A LCC 9 P ? ? A LCC 8 A LCC 9 1_555 ? ? ? ? ? ? ? 1.656 ? ? covale5 covale both ? A LCC 9 "O3'" ? ? ? 1_555 A G 10 P ? ? A LCC 9 A G 10 1_555 ? ? ? ? ? ? ? 1.704 ? ? covale6 covale one ? B 8OS 1 O4 ? ? ? 1_555 B C 2 P ? ? B 8OS 1 B C 2 1_555 ? ? ? ? ? ? ? 1.681 ? ? hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 3 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 3 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 4 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 5 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 5 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 5 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 5BU 6 N3 ? ? ? 1_555 B A 3 N1 ? ? A 5BU 6 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 5BU 6 O4 ? ? ? 1_555 B A 3 N6 ? ? A 5BU 6 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 7 B C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 10 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 10 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 10 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 11 N1 ? ? ? 1_555 A U 24 N3 ? ? A A 11 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 11 N6 ? ? ? 1_555 A U 24 O4 ? ? A A 11 A U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 12 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 13 A G 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 14 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 14 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 14 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 14 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 16 N2 ? ? ? 1_555 A A 19 N7 ? ? A G 16 A A 19 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B 8OS 101 ? 8 'binding site for residue 8OS B 101' AC2 Software A LCC 8 ? 5 'binding site for residues LCC A 8 and LCC A 9' # 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 8 G A 2 ? G A 2 . ? 6_567 ? 2 AC1 8 A A 3 ? A A 3 . ? 6_567 ? 3 AC1 8 LCC A 9 ? LCC A 9 . ? 1_555 ? 4 AC1 8 G A 10 ? G A 10 . ? 1_555 ? 5 AC1 8 A A 17 ? A A 17 . ? 3_744 ? 6 AC1 8 C A 25 ? C A 25 . ? 1_555 ? 7 AC1 8 8OS B 1 ? 8OS B 1 . ? 1_555 ? 8 AC1 8 C B 7 ? C B 7 . ? 6_567 ? 9 AC2 5 G A 2 ? G A 2 . ? 6_567 ? 10 AC2 5 G A 7 ? G A 7 . ? 1_555 ? 11 AC2 5 G A 10 ? G A 10 . ? 1_555 ? 12 AC2 5 8OS B 1 ? 8OS B 1 . ? 1_555 ? 13 AC2 5 8OS C . ? 8OS B 101 . ? 1_555 ? # _atom_sites.entry_id 5UX3 _atom_sites.fract_transf_matrix[1][1] 0.021493 _atom_sites.fract_transf_matrix[1][2] 0.000000 _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] 0.021493 _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] 0.006372 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol BR C 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 U 1 1 1 U U 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 G 5 5 5 G G A . n A 1 6 5BU 6 6 6 5BU 5BU A . n A 1 7 G 7 7 7 G G A . n A 1 8 LCC 8 8 8 LCC LCC A . n A 1 9 LCC 9 9 9 LCC LCC A . n A 1 10 G 10 10 10 G G A . n A 1 11 A 11 11 11 A A A . n A 1 12 G 12 12 12 G G A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 A 19 19 19 A A 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 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n A 1 24 U 24 24 24 U U A . n A 1 25 C 25 25 25 C C A . n B 2 1 8OS 1 1 1 8OS rG B . n B 2 2 C 2 2 2 C C B . n B 2 3 A 3 3 3 A A B . n B 2 4 C 4 4 4 C C B . n B 2 5 C 5 5 5 C C B . n B 2 6 U 6 6 6 U U B . n B 2 7 C 7 7 7 C C B . n B 2 8 A 8 8 8 A A B . 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 C 3 8OS 1 101 1 8OS rG B . D 4 HOH 1 101 1 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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1600 ? 1 MORE 5 ? 1 'SSA (A^2)' 6290 ? # _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 2018-02-21 2 'Structure model' 1 1 2018-03-14 3 'Structure model' 1 2 2020-01-01 4 'Structure model' 1 3 2023-10-04 # _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' 'Author supporting evidence' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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' pdbx_audit_support 3 4 'Structure model' chem_comp_atom 4 4 'Structure model' chem_comp_bond 5 4 'Structure model' database_2 6 4 '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.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.title' 5 3 'Structure model' '_pdbx_audit_support.funding_organization' 6 4 'Structure model' '_database_2.pdbx_DOI' 7 4 'Structure model' '_database_2.pdbx_database_accession' # 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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0135 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? v3.0 4 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 C _pdbx_validate_symm_contact.auth_seq_id_1 25 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 "O3'" _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 A _pdbx_validate_symm_contact.auth_seq_id_2 8 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 6_567 _pdbx_validate_symm_contact.dist 2.11 # 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 "O3'" A 5BU 6 ? ? P A G 7 ? ? 1.705 1.607 0.098 0.012 Y 2 1 P A G 7 ? ? OP2 A G 7 ? ? 1.657 1.485 0.172 0.017 N 3 1 P A G 7 ? ? "O5'" A G 7 ? ? 1.715 1.593 0.122 0.010 N 4 1 "O3'" A LCC 9 ? ? P A G 10 ? ? 1.704 1.607 0.097 0.012 Y # 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 "O3'" A G 5 ? ? P A 5BU 6 ? ? "O5'" A 5BU 6 ? ? 77.41 104.00 -26.59 1.90 Y 2 1 "O3'" A G 5 ? ? P A 5BU 6 ? ? OP2 A 5BU 6 ? ? 121.47 110.50 10.97 1.10 Y 3 1 "O3'" A 5BU 6 ? ? P A G 7 ? ? OP2 A G 7 ? ? 121.55 110.50 11.05 1.10 Y 4 1 "O5'" A G 7 ? ? P A G 7 ? ? OP1 A G 7 ? ? 119.52 110.70 8.82 1.20 N 5 1 "O5'" A G 7 ? ? P A G 7 ? ? OP2 A G 7 ? ? 87.13 105.70 -18.57 0.90 N 6 1 P A G 7 ? ? "O5'" A G 7 ? ? "C5'" A G 7 ? ? 103.49 120.90 -17.41 1.60 N 7 1 "C3'" A LCC 8 ? ? "O3'" A LCC 8 ? ? P A LCC 9 ? ? 128.10 119.70 8.40 1.20 Y 8 1 "O3'" A LCC 8 ? ? P A LCC 9 ? ? "O5'" A LCC 9 ? ? 90.85 104.00 -13.15 1.90 Y 9 1 "C3'" A LCC 9 ? ? "O3'" A LCC 9 ? ? P A G 10 ? ? 138.35 119.70 18.65 1.20 Y 10 1 "O3'" A LCC 9 ? ? P A G 10 ? ? OP1 A G 10 ? ? 138.45 110.50 27.95 1.10 Y # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id 5BU _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 6 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id O2 _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id A _pdbx_unobs_or_zero_occ_atoms.label_comp_id 5BU _pdbx_unobs_or_zero_occ_atoms.label_seq_id 6 _pdbx_unobs_or_zero_occ_atoms.label_atom_id O2 # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 8OS O1 O N N 35 8OS C1 C N N 36 8OS N1 N N N 37 8OS C2 C N N 38 8OS N2 N N N 39 8OS N3 N N N 40 8OS C3 C Y N 41 8OS C4 C Y N 42 8OS N4 N Y N 43 8OS C5 C Y N 44 8OS N5 N Y N 45 8OS C6 C N R 46 8OS O2 O N N 47 8OS C7 C N R 48 8OS O3 O N N 49 8OS C8 C N S 50 8OS O4 O N N 51 8OS C9 C N R 52 8OS C10 C N N 53 8OS O5 O N N 54 8OS P1 P N N 55 8OS O6 O N N 56 8OS O7 O N N 57 8OS C11 C Y N 58 8OS N6 N Y N 59 8OS C12 C Y N 60 8OS N7 N Y N 61 8OS C13 C Y N 62 8OS C14 C N N 63 8OS H1 H N N 64 8OS H2 H N N 65 8OS H3 H N N 66 8OS H4 H N N 67 8OS H5 H N N 68 8OS H6 H N N 69 8OS H7 H N N 70 8OS H8 H N N 71 8OS H9 H N N 72 8OS H10 H N N 73 8OS H11 H N N 74 8OS H12 H N N 75 8OS H13 H N N 76 8OS H14 H N N 77 8OS H15 H N N 78 8OS H17 H N N 79 8OS H18 H N N 80 8OS H19 H N N 81 A OP3 O N N 82 A P P N N 83 A OP1 O N N 84 A OP2 O N N 85 A "O5'" O N N 86 A "C5'" C N N 87 A "C4'" C N R 88 A "O4'" O N N 89 A "C3'" C N S 90 A "O3'" O N N 91 A "C2'" C N R 92 A "O2'" O N N 93 A "C1'" C N R 94 A N9 N Y N 95 A C8 C Y N 96 A N7 N Y N 97 A C5 C Y N 98 A C6 C Y N 99 A N6 N N N 100 A N1 N Y N 101 A C2 C Y N 102 A N3 N Y N 103 A C4 C Y N 104 A HOP3 H N N 105 A HOP2 H N N 106 A "H5'" H N N 107 A "H5''" H N N 108 A "H4'" H N N 109 A "H3'" H N N 110 A "HO3'" H N N 111 A "H2'" H N N 112 A "HO2'" H N N 113 A "H1'" H N N 114 A H8 H N N 115 A H61 H N N 116 A H62 H N N 117 A H2 H N N 118 C OP3 O N N 119 C P P N N 120 C OP1 O N N 121 C OP2 O N N 122 C "O5'" O N N 123 C "C5'" C N N 124 C "C4'" C N R 125 C "O4'" O N N 126 C "C3'" C N S 127 C "O3'" O N N 128 C "C2'" C N R 129 C "O2'" O N N 130 C "C1'" C N R 131 C N1 N N N 132 C C2 C N N 133 C O2 O N N 134 C N3 N N N 135 C C4 C N N 136 C N4 N N N 137 C C5 C N N 138 C C6 C N N 139 C HOP3 H N N 140 C HOP2 H N N 141 C "H5'" H N N 142 C "H5''" H N N 143 C "H4'" H N N 144 C "H3'" H N N 145 C "HO3'" H N N 146 C "H2'" H N N 147 C "HO2'" H N N 148 C "H1'" H N N 149 C H41 H N N 150 C H42 H N N 151 C H5 H N N 152 C H6 H N N 153 G OP3 O N N 154 G P P N N 155 G OP1 O N N 156 G OP2 O N N 157 G "O5'" O N N 158 G "C5'" C N N 159 G "C4'" C N R 160 G "O4'" O N N 161 G "C3'" C N S 162 G "O3'" O N N 163 G "C2'" C N R 164 G "O2'" O N N 165 G "C1'" C N R 166 G N9 N Y N 167 G C8 C Y N 168 G N7 N Y N 169 G C5 C Y N 170 G C6 C N N 171 G O6 O N N 172 G N1 N N N 173 G C2 C N N 174 G N2 N N N 175 G N3 N N N 176 G C4 C Y N 177 G HOP3 H N N 178 G HOP2 H N N 179 G "H5'" H N N 180 G "H5''" H N N 181 G "H4'" H N N 182 G "H3'" H N N 183 G "HO3'" H N N 184 G "H2'" H N N 185 G "HO2'" H N N 186 G "H1'" H N N 187 G H8 H N N 188 G H1 H N N 189 G H21 H N N 190 G H22 H N N 191 HOH O O N N 192 HOH H1 H N N 193 HOH H2 H N N 194 LCC "O5'" O N N 195 LCC "C5'" C N N 196 LCC "C4'" C N R 197 LCC "O4'" O N N 198 LCC "C1'" C N R 199 LCC N1 N N N 200 LCC C6 C N N 201 LCC C5 C N N 202 LCC C5M C N N 203 LCC C4 C N N 204 LCC N4 N N N 205 LCC N3 N N N 206 LCC C2 C N N 207 LCC O2 O N N 208 LCC "C3'" C N S 209 LCC "C2'" C N R 210 LCC "O2'" O N N 211 LCC "O3'" O N N 212 LCC "C6'" C N N 213 LCC P P N N 214 LCC O1P O N N 215 LCC O2P O N N 216 LCC OXT O N N 217 LCC "H5'1" H N N 218 LCC "H5'2" H N N 219 LCC "H1'" H N N 220 LCC H6 H N N 221 LCC H5M1 H N N 222 LCC H5M2 H N N 223 LCC H5M3 H N N 224 LCC H41 H N N 225 LCC H42 H N N 226 LCC "H3'" H N N 227 LCC "H2'1" H N N 228 LCC H3T H N N 229 LCC "H6'1" H N N 230 LCC "H6'2" H N N 231 LCC H1P H N N 232 LCC HXT H N N 233 U OP3 O N N 234 U P P N N 235 U OP1 O N N 236 U OP2 O N N 237 U "O5'" O N N 238 U "C5'" C N N 239 U "C4'" C N R 240 U "O4'" O N N 241 U "C3'" C N S 242 U "O3'" O N N 243 U "C2'" C N R 244 U "O2'" O N N 245 U "C1'" C N R 246 U N1 N N N 247 U C2 C N N 248 U O2 O N N 249 U N3 N N N 250 U C4 C N N 251 U O4 O N N 252 U C5 C N N 253 U C6 C N N 254 U HOP3 H N N 255 U HOP2 H N N 256 U "H5'" H N N 257 U "H5''" H N N 258 U "H4'" H N N 259 U "H3'" H N N 260 U "HO3'" H N N 261 U "H2'" H N N 262 U "HO2'" H N N 263 U "H1'" H N N 264 U H3 H N N 265 U H5 H N N 266 U H6 H N N 267 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 8OS C14 C13 sing N N 36 8OS O7 P1 doub N N 37 8OS C13 N7 sing Y N 38 8OS C13 C11 doub Y N 39 8OS C10 C9 sing N N 40 8OS C10 O5 sing N N 41 8OS N7 C12 doub Y N 42 8OS O4 C8 sing N N 43 8OS P1 C11 sing N N 44 8OS P1 O5 sing N N 45 8OS P1 O6 sing N N 46 8OS C11 N6 sing Y N 47 8OS C9 C8 sing N N 48 8OS C9 O2 sing N N 49 8OS C8 C7 sing N N 50 8OS C12 N6 sing Y N 51 8OS O2 C6 sing N N 52 8OS O3 C7 sing N N 53 8OS C7 C6 sing N N 54 8OS C6 N5 sing N N 55 8OS C5 N5 sing Y N 56 8OS C5 N4 doub Y N 57 8OS N5 C3 sing Y N 58 8OS N4 C4 sing Y N 59 8OS C3 N3 sing N N 60 8OS C3 C4 doub Y N 61 8OS N3 C2 doub N N 62 8OS C4 C1 sing N N 63 8OS C2 N2 sing N N 64 8OS C2 N1 sing N N 65 8OS C1 N1 sing N N 66 8OS C1 O1 doub N N 67 8OS N1 H1 sing N N 68 8OS N2 H2 sing N N 69 8OS N2 H3 sing N N 70 8OS C5 H4 sing N N 71 8OS C6 H5 sing N N 72 8OS C7 H6 sing N N 73 8OS O3 H7 sing N N 74 8OS C8 H8 sing N N 75 8OS O4 H9 sing N N 76 8OS C9 H10 sing N N 77 8OS C10 H11 sing N N 78 8OS C10 H12 sing N N 79 8OS O6 H13 sing N N 80 8OS N6 H14 sing N N 81 8OS C12 H15 sing N N 82 8OS C14 H17 sing N N 83 8OS C14 H18 sing N N 84 8OS C14 H19 sing N N 85 A OP3 P sing N N 86 A OP3 HOP3 sing N N 87 A P OP1 doub N N 88 A P OP2 sing N N 89 A P "O5'" sing N N 90 A OP2 HOP2 sing N N 91 A "O5'" "C5'" sing N N 92 A "C5'" "C4'" sing N N 93 A "C5'" "H5'" sing N N 94 A "C5'" "H5''" sing N N 95 A "C4'" "O4'" sing N N 96 A "C4'" "C3'" sing N N 97 A "C4'" "H4'" sing N N 98 A "O4'" "C1'" sing N N 99 A "C3'" "O3'" sing N N 100 A "C3'" "C2'" sing N N 101 A "C3'" "H3'" sing N N 102 A "O3'" "HO3'" sing N N 103 A "C2'" "O2'" sing N N 104 A "C2'" "C1'" sing N N 105 A "C2'" "H2'" sing N N 106 A "O2'" "HO2'" sing N N 107 A "C1'" N9 sing N N 108 A "C1'" "H1'" sing N N 109 A N9 C8 sing Y N 110 A N9 C4 sing Y N 111 A C8 N7 doub Y N 112 A C8 H8 sing N N 113 A N7 C5 sing Y N 114 A C5 C6 sing Y N 115 A C5 C4 doub Y N 116 A C6 N6 sing N N 117 A C6 N1 doub Y N 118 A N6 H61 sing N N 119 A N6 H62 sing N N 120 A N1 C2 sing Y N 121 A C2 N3 doub Y N 122 A C2 H2 sing N N 123 A N3 C4 sing Y N 124 C OP3 P sing N N 125 C OP3 HOP3 sing N N 126 C P OP1 doub N N 127 C P OP2 sing N N 128 C P "O5'" sing N N 129 C OP2 HOP2 sing N N 130 C "O5'" "C5'" sing N N 131 C "C5'" "C4'" sing N N 132 C "C5'" "H5'" sing N N 133 C "C5'" "H5''" sing N N 134 C "C4'" "O4'" sing N N 135 C "C4'" "C3'" sing N N 136 C "C4'" "H4'" sing N N 137 C "O4'" "C1'" sing N N 138 C "C3'" "O3'" sing N N 139 C "C3'" "C2'" sing N N 140 C "C3'" "H3'" sing N N 141 C "O3'" "HO3'" sing N N 142 C "C2'" "O2'" sing N N 143 C "C2'" "C1'" sing N N 144 C "C2'" "H2'" sing N N 145 C "O2'" "HO2'" sing N N 146 C "C1'" N1 sing N N 147 C "C1'" "H1'" sing N N 148 C N1 C2 sing N N 149 C N1 C6 sing N N 150 C C2 O2 doub N N 151 C C2 N3 sing N N 152 C N3 C4 doub N N 153 C C4 N4 sing N N 154 C C4 C5 sing N N 155 C N4 H41 sing N N 156 C N4 H42 sing N N 157 C C5 C6 doub N N 158 C C5 H5 sing N N 159 C C6 H6 sing N N 160 G OP3 P sing N N 161 G OP3 HOP3 sing N N 162 G P OP1 doub N N 163 G P OP2 sing N N 164 G P "O5'" sing N N 165 G OP2 HOP2 sing N N 166 G "O5'" "C5'" sing N N 167 G "C5'" "C4'" sing N N 168 G "C5'" "H5'" sing N N 169 G "C5'" "H5''" sing N N 170 G "C4'" "O4'" sing N N 171 G "C4'" "C3'" sing N N 172 G "C4'" "H4'" sing N N 173 G "O4'" "C1'" sing N N 174 G "C3'" "O3'" sing N N 175 G "C3'" "C2'" sing N N 176 G "C3'" "H3'" sing N N 177 G "O3'" "HO3'" sing N N 178 G "C2'" "O2'" sing N N 179 G "C2'" "C1'" sing N N 180 G "C2'" "H2'" sing N N 181 G "O2'" "HO2'" sing N N 182 G "C1'" N9 sing N N 183 G "C1'" "H1'" sing N N 184 G N9 C8 sing Y N 185 G N9 C4 sing Y N 186 G C8 N7 doub Y N 187 G C8 H8 sing N N 188 G N7 C5 sing Y N 189 G C5 C6 sing N N 190 G C5 C4 doub Y N 191 G C6 O6 doub N N 192 G C6 N1 sing N N 193 G N1 C2 sing N N 194 G N1 H1 sing N N 195 G C2 N2 sing N N 196 G C2 N3 doub N N 197 G N2 H21 sing N N 198 G N2 H22 sing N N 199 G N3 C4 sing N N 200 HOH O H1 sing N N 201 HOH O H2 sing N N 202 LCC "O5'" "C5'" sing N N 203 LCC "O5'" P sing N N 204 LCC "C5'" "C4'" sing N N 205 LCC "C5'" "H5'1" sing N N 206 LCC "C5'" "H5'2" sing N N 207 LCC "C4'" "O4'" sing N N 208 LCC "C4'" "C3'" sing N N 209 LCC "C4'" "C6'" sing N N 210 LCC "O4'" "C1'" sing N N 211 LCC "C1'" N1 sing N N 212 LCC "C1'" "C2'" sing N N 213 LCC "C1'" "H1'" sing N N 214 LCC N1 C6 sing N N 215 LCC N1 C2 sing N N 216 LCC C6 C5 doub N N 217 LCC C6 H6 sing N N 218 LCC C5 C5M sing N N 219 LCC C5 C4 sing N N 220 LCC C5M H5M1 sing N N 221 LCC C5M H5M2 sing N N 222 LCC C5M H5M3 sing N N 223 LCC C4 N4 sing N N 224 LCC C4 N3 doub N N 225 LCC N4 H41 sing N N 226 LCC N4 H42 sing N N 227 LCC N3 C2 sing N N 228 LCC C2 O2 doub N N 229 LCC "C3'" "C2'" sing N N 230 LCC "C3'" "O3'" sing N N 231 LCC "C3'" "H3'" sing N N 232 LCC "C2'" "O2'" sing N N 233 LCC "C2'" "H2'1" sing N N 234 LCC "O2'" "C6'" sing N N 235 LCC "O3'" H3T sing N N 236 LCC "C6'" "H6'1" sing N N 237 LCC "C6'" "H6'2" sing N N 238 LCC P O1P sing N N 239 LCC P O2P doub N N 240 LCC P OXT sing N N 241 LCC O1P H1P sing N N 242 LCC OXT HXT sing N N 243 U OP3 P sing N N 244 U OP3 HOP3 sing N N 245 U P OP1 doub N N 246 U P OP2 sing N N 247 U P "O5'" sing N N 248 U OP2 HOP2 sing N N 249 U "O5'" "C5'" sing N N 250 U "C5'" "C4'" sing N N 251 U "C5'" "H5'" sing N N 252 U "C5'" "H5''" sing N N 253 U "C4'" "O4'" sing N N 254 U "C4'" "C3'" sing N N 255 U "C4'" "H4'" sing N N 256 U "O4'" "C1'" sing N N 257 U "C3'" "O3'" sing N N 258 U "C3'" "C2'" sing N N 259 U "C3'" "H3'" sing N N 260 U "O3'" "HO3'" sing N N 261 U "C2'" "O2'" sing N N 262 U "C2'" "C1'" sing N N 263 U "C2'" "H2'" sing N N 264 U "O2'" "HO2'" sing N N 265 U "C1'" N1 sing N N 266 U "C1'" "H1'" sing N N 267 U N1 C2 sing N N 268 U N1 C6 sing N N 269 U C2 O2 doub N N 270 U C2 N3 sing N N 271 U N3 C4 sing N N 272 U N3 H3 sing N N 273 U C4 O4 doub N N 274 U C4 C5 sing N N 275 U C5 C6 doub N N 276 U C5 H5 sing N N 277 U C6 H6 sing N N 278 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5UX3 'a-form double helix' 5UX3 tetraloop 5UX3 'mismatched base pair' # 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 2 1_555 B C 7 1_555 -0.130 -0.085 -0.177 -8.848 -5.075 -1.248 1 A_G2:C7_B A 2 ? B 7 ? 19 1 1 A A 3 1_555 B U 6 1_555 0.101 -0.201 -0.262 -7.459 -15.654 3.879 2 A_A3:U6_B A 3 ? B 6 ? 20 1 1 A G 4 1_555 B C 5 1_555 -0.190 -0.101 0.017 -4.044 -9.573 -0.276 3 A_G4:C5_B A 4 ? B 5 ? 19 1 1 A G 5 1_555 B C 4 1_555 0.038 -0.118 0.144 -7.814 -13.333 0.726 4 A_G5:C4_B A 5 ? B 4 ? 19 1 1 A 5BU 6 1_555 B A 3 1_555 -0.061 -0.110 0.411 -5.221 -10.848 -0.710 5 A_5BU6:A3_B A 6 ? B 3 ? 20 1 1 A G 7 1_555 B C 2 1_555 0.012 0.008 0.521 -5.948 -11.141 -2.679 6 A_G7:C2_B A 7 ? B 2 ? 19 1 1 A G 10 1_555 A C 25 1_555 -0.058 -0.025 -0.103 -6.066 -16.421 1.647 7 A_G10:C25_A A 10 ? A 25 ? 19 1 1 A A 11 1_555 A U 24 1_555 -0.324 -0.153 0.092 -2.772 -10.928 2.209 8 A_A11:U24_A A 11 ? A 24 ? 20 1 1 A G 12 1_555 A C 23 1_555 -0.177 -0.049 -0.425 -9.937 -21.303 5.544 9 A_G12:C23_A A 12 ? A 23 ? 19 1 1 A C 13 1_555 A G 22 1_555 0.168 -0.032 -0.120 -3.428 -13.674 3.385 10 A_C13:G22_A A 13 ? A 22 ? 19 1 1 A G 14 1_555 A C 21 1_555 0.084 0.008 -0.277 -4.915 -0.964 0.403 11 A_G14:C21_A A 14 ? A 21 ? 19 1 1 A C 15 1_555 A G 20 1_555 0.297 0.012 -0.058 0.208 9.857 1.810 12 A_C15:G20_A A 15 ? A 20 ? 19 1 1 A G 16 1_555 A A 19 1_555 7.020 -5.667 0.768 14.079 5.529 -15.368 13 A_G16:A19_A A 16 ? A 19 ? ? ? # 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 2 1_555 B C 7 1_555 A A 3 1_555 B U 6 1_555 0.466 -1.311 3.511 -0.214 8.175 32.101 -3.714 -0.855 3.090 14.492 0.379 33.099 1 AA_G2A3:U6C7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A A 3 1_555 B U 6 1_555 A G 4 1_555 B C 5 1_555 -0.097 -1.737 3.149 -1.474 8.674 31.167 -4.486 -0.059 2.586 15.755 2.676 32.356 2 AA_A3G4:C5U6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A G 4 1_555 B C 5 1_555 A G 5 1_555 B C 4 1_555 0.969 -2.386 3.187 3.345 5.632 27.471 -6.098 -1.271 2.749 11.651 -6.919 28.227 3 AA_G4G5:C4C5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A G 5 1_555 B C 4 1_555 A 5BU 6 1_555 B A 3 1_555 -0.282 -1.680 3.160 -0.632 2.107 32.526 -3.341 0.397 3.053 3.756 1.127 32.598 4 AA_G55BU6:A3C4_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A 5BU 6 1_555 B A 3 1_555 A G 7 1_555 B C 2 1_555 0.060 -1.714 3.147 0.433 2.404 33.263 -3.363 -0.036 3.020 4.192 -0.756 33.350 5 AA_5BU6G7:C2A3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A G 10 1_555 A C 25 1_555 A A 11 1_555 A U 24 1_555 -0.008 -1.118 3.076 -4.759 9.631 29.625 -3.664 -0.777 2.566 18.103 8.945 31.472 6 AA_G10A11:U24C25_AA A 10 ? A 25 ? A 11 ? A 24 ? 1 A A 11 1_555 A U 24 1_555 A G 12 1_555 A C 23 1_555 0.267 -1.408 3.553 3.973 10.208 32.614 -4.027 0.188 3.001 17.571 -6.838 34.357 7 AA_A11G12:C23U24_AA A 11 ? A 24 ? A 12 ? A 23 ? 1 A G 12 1_555 A C 23 1_555 A C 13 1_555 A G 22 1_555 0.068 -1.033 3.195 -1.390 2.703 34.009 -2.172 -0.329 3.101 4.609 2.371 34.140 8 AA_G12C13:G22C23_AA A 12 ? A 23 ? A 13 ? A 22 ? 1 A C 13 1_555 A G 22 1_555 A G 14 1_555 A C 21 1_555 0.635 -2.177 3.296 1.614 6.516 28.850 -5.557 -0.921 2.778 12.860 -3.185 29.605 9 AA_C13G14:C21G22_AA A 13 ? A 22 ? A 14 ? A 21 ? 1 A G 14 1_555 A C 21 1_555 A C 15 1_555 A G 20 1_555 0.176 -2.501 3.305 -0.465 0.776 27.619 -5.424 -0.481 3.232 1.626 0.974 27.633 10 AA_G14C15:G20C21_AA A 14 ? A 21 ? A 15 ? A 20 ? 1 A C 15 1_555 A G 20 1_555 A G 16 1_555 A A 19 1_555 -1.855 -1.184 2.777 -3.117 7.022 55.807 -1.590 1.818 2.714 7.463 3.313 56.291 11 AA_C15G16:A19G20_AA A 15 ? A 20 ? A 16 ? A 19 ? # _pdbx_audit_support.funding_organization 'National Aeronautic Space Administration (NASA, United States)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 "5'-O-[(S)-hydroxy(4-methyl-1H-imidazol-5-yl)phosphoryl]guanosine" 8OS 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 4FNJ _pdbx_initial_refinement_model.details ? #