data_5VXQ # _entry.id 5VXQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 5VXQ pdb_00005vxq 10.2210/pdb5vxq/pdb WWPDB D_1000227261 ? ? # 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 2017-08-16 2 'Structure model' 1 1 2017-08-23 3 'Structure model' 1 2 2017-10-11 4 'Structure model' 1 3 2024-03-13 # _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' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' # 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 2 'Structure model' citation_author 3 3 'Structure model' citation 4 3 'Structure model' citation_author 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 'Structure model' database_2 # 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.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.title' 8 2 'Structure model' '_citation.year' 9 3 'Structure model' '_citation.journal_volume' 10 3 'Structure model' '_citation.page_first' 11 3 'Structure model' '_citation.page_last' 12 3 'Structure model' '_citation.pdbx_database_id_PubMed' 13 3 'Structure model' '_citation.title' 14 3 'Structure model' '_citation_author.name' 15 4 'Structure model' '_database_2.pdbx_DOI' 16 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5VXQ _pdbx_database_status.recvd_initial_deposition_date 2017-05-23 _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 'Xie, J.' 1 ? 'Chen, Y.' 2 ? 'Wei, X.' 3 ? 'Kozlov, G.' 4 ? 'Gehring, K.' 5 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 45 _citation.language ? _citation.page_first 10321 _citation.page_last 10331 _citation.title ;Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA. ; _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkx713 _citation.pdbx_database_id_PubMed 28973475 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Copp, W.' 1 ? primary 'Denisov, A.Y.' 2 ? primary 'Xie, J.' 3 ? primary 'Noronha, A.M.' 4 ? primary 'Liczner, C.' 5 ? primary 'Safaee, N.' 6 ? primary 'Wilds, C.J.' 7 ? primary 'Gehring, K.' 8 ? # 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 ;DNA/RNA (5'-R(*AP*AP*AP*AP*A)-D(P*A)-R(P*AP*AP*AP*AP*A)-3') ; 3560.307 2 ? ? ? 'modified RNA duplex' 2 non-polymer syn 'AMMONIUM ION' 18.038 18 ? ? ? ? 3 water nat water 18.015 71 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'AAAAA(DA)AAAAA' _entity_poly.pdbx_seq_one_letter_code_can AAAAAAAAAAA _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'AMMONIUM ION' NH4 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 A n 1 2 A n 1 3 A n 1 4 A n 1 5 A n 1 6 DA n 1 7 A n 1 8 A n 1 9 A n 1 10 A n 1 11 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 11 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 HOH non-polymer . WATER ? 'H2 O' 18.015 NH4 non-polymer . 'AMMONIUM ION' ? 'H4 N 1' 18.038 # 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 A 1 1 1 A A A . n A 1 2 A 2 2 2 A A A . n A 1 3 A 3 3 3 A A A . n A 1 4 A 4 4 4 A A A . n A 1 5 A 5 5 5 A A A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 A 7 7 7 A A A . n A 1 8 A 8 8 8 A A A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 A 11 11 11 A A A . n B 1 1 A 1 12 12 A A B . n B 1 2 A 2 13 13 A A B . n B 1 3 A 3 14 14 A A B . n B 1 4 A 4 15 15 A A B . n B 1 5 A 5 16 16 A A B . n B 1 6 DA 6 17 17 DA DA B . n B 1 7 A 7 18 18 A A B . n B 1 8 A 8 19 19 A A B . n B 1 9 A 9 20 20 A A B . n B 1 10 A 10 21 21 A A B . n B 1 11 A 11 22 22 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 2 NH4 1 101 25 NH4 NH4 A . D 2 NH4 1 102 30 NH4 NH4 A . E 2 NH4 1 103 31 NH4 NH4 A . F 2 NH4 1 104 32 NH4 NH4 A . G 2 NH4 1 105 33 NH4 NH4 A . H 2 NH4 1 106 34 NH4 NH4 A . I 2 NH4 1 107 36 NH4 NH4 A . J 2 NH4 1 108 37 NH4 NH4 A . K 2 NH4 1 109 38 NH4 NH4 A . L 2 NH4 1 110 39 NH4 NH4 A . M 2 NH4 1 111 40 NH4 NH4 A . N 2 NH4 1 112 41 NH4 NH4 A . O 2 NH4 1 101 23 NH4 NH4 B . P 2 NH4 1 102 24 NH4 NH4 B . Q 2 NH4 1 103 26 NH4 NH4 B . R 2 NH4 1 104 27 NH4 NH4 B . S 2 NH4 1 105 28 NH4 NH4 B . T 2 NH4 1 106 29 NH4 NH4 B . U 3 HOH 1 201 88 HOH HOH A . U 3 HOH 2 202 53 HOH HOH A . U 3 HOH 3 203 87 HOH HOH A . U 3 HOH 4 204 47 HOH HOH A . U 3 HOH 5 205 43 HOH HOH A . U 3 HOH 6 206 106 HOH HOH A . U 3 HOH 7 207 92 HOH HOH A . U 3 HOH 8 208 64 HOH HOH A . U 3 HOH 9 209 80 HOH HOH A . U 3 HOH 10 210 45 HOH HOH A . U 3 HOH 11 211 66 HOH HOH A . U 3 HOH 12 212 55 HOH HOH A . U 3 HOH 13 213 83 HOH HOH A . U 3 HOH 14 214 85 HOH HOH A . U 3 HOH 15 215 65 HOH HOH A . U 3 HOH 16 216 82 HOH HOH A . U 3 HOH 17 217 81 HOH HOH A . U 3 HOH 18 218 49 HOH HOH A . U 3 HOH 19 219 107 HOH HOH A . U 3 HOH 20 220 73 HOH HOH A . U 3 HOH 21 221 79 HOH HOH A . U 3 HOH 22 222 67 HOH HOH A . U 3 HOH 23 223 51 HOH HOH A . U 3 HOH 24 224 93 HOH HOH A . U 3 HOH 25 225 99 HOH HOH A . U 3 HOH 26 226 101 HOH HOH A . U 3 HOH 27 227 61 HOH HOH A . U 3 HOH 28 228 56 HOH HOH A . U 3 HOH 29 229 77 HOH HOH A . U 3 HOH 30 230 98 HOH HOH A . U 3 HOH 31 231 70 HOH HOH A . U 3 HOH 32 232 75 HOH HOH A . U 3 HOH 33 233 95 HOH HOH A . U 3 HOH 34 234 111 HOH HOH A . U 3 HOH 35 235 104 HOH HOH A . U 3 HOH 36 236 76 HOH HOH A . U 3 HOH 37 237 78 HOH HOH A . U 3 HOH 38 238 42 HOH HOH A . V 3 HOH 1 201 109 HOH HOH B . V 3 HOH 2 202 69 HOH HOH B . V 3 HOH 3 203 46 HOH HOH B . V 3 HOH 4 204 72 HOH HOH B . V 3 HOH 5 205 54 HOH HOH B . V 3 HOH 6 206 112 HOH HOH B . V 3 HOH 7 207 108 HOH HOH B . V 3 HOH 8 208 60 HOH HOH B . V 3 HOH 9 209 100 HOH HOH B . V 3 HOH 10 210 74 HOH HOH B . V 3 HOH 11 211 62 HOH HOH B . V 3 HOH 12 212 90 HOH HOH B . V 3 HOH 13 213 48 HOH HOH B . V 3 HOH 14 214 84 HOH HOH B . V 3 HOH 15 215 63 HOH HOH B . V 3 HOH 16 216 97 HOH HOH B . V 3 HOH 17 217 71 HOH HOH B . V 3 HOH 18 218 44 HOH HOH B . V 3 HOH 19 219 57 HOH HOH B . V 3 HOH 20 220 68 HOH HOH B . V 3 HOH 21 221 58 HOH HOH B . V 3 HOH 22 222 102 HOH HOH B . V 3 HOH 23 223 110 HOH HOH B . V 3 HOH 24 224 59 HOH HOH B . V 3 HOH 25 225 86 HOH HOH B . V 3 HOH 26 226 52 HOH HOH B . V 3 HOH 27 227 105 HOH HOH B . V 3 HOH 28 228 94 HOH HOH B . V 3 HOH 29 229 89 HOH HOH B . V 3 HOH 30 230 103 HOH HOH B . V 3 HOH 31 231 91 HOH HOH B . V 3 HOH 32 232 96 HOH HOH B . V 3 HOH 33 233 50 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.9 1 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.9 2 # _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 5VXQ _cell.details ? _cell.formula_units_Z ? _cell.length_a 22.799 _cell.length_a_esd ? _cell.length_b 22.799 _cell.length_b_esd ? _cell.length_c 164.071 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 16 _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 5VXQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' _symmetry.pdbx_full_space_group_name_H-M ? # _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 5VXQ _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 1.50 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 17.84 _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 'HANGING DROP, VAPOR DIFFUSION' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.5 uL 5-rA5-dA-rA5 and RRM23 (98-269) in 10 mM HEPES, 100 mM sodium chloride, 2 mM DTT, pH 7.0 + 0.5 uL 1.6 M ammonium sulfate, 0.1 M citric acid, pH 5.0 ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 77 _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 'RAYONIX MX-300' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-05-01 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'double crystal Si(111)' _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 1.28206 _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 'CLSI BEAMLINE 08ID-1' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.28206 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 08ID-1 _diffrn_source.pdbx_synchrotron_site CLSI # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5VXQ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.002 _reflns.d_resolution_low 22.58 _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 23843 _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 96.4 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 1 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 17.65 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.002 _reflns_shell.d_res_low ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all ? _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _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 ? _refine.B_iso_mean ? _refine.B_iso_min ? _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 5VXQ _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 1.002 _refine.ls_d_res_low 22.58 _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 23843 _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.4 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free 0.1598 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1285 _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 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _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 ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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 ? _refine.overall_SU_ML ? _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 LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 476 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 565 _refine_hist.d_res_high 1.002 _refine_hist.d_res_low 22.58 # _struct.entry_id 5VXQ _struct.title 'X-Ray crystallography structure of the parallel stranded duplex formed by 5-rA5-dA-rA5' _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 5VXQ _struct_keywords.text 'RNA, DNA, duplex' _struct_keywords.pdbx_keywords 'RNA, DNA' # 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 1 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 2 ? Q N N 2 ? R N N 2 ? S N N 2 ? T N N 2 ? U N N 3 ? V N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5VXQ _struct_ref.pdbx_db_accession 5VXQ _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 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 5VXQ A 1 ? 11 ? 5VXQ 1 ? 11 ? 1 11 2 1 5VXQ B 1 ? 11 ? 5VXQ 12 ? 22 ? 12 22 # _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 # 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)' 4650 ? 1 MORE 3 ? 1 'SSA (A^2)' 2740 ? # _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'isothermal titration calorimetry' _pdbx_struct_assembly_auth_evidence.details ? # _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_ _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 hydrog1 hydrog ? ? A A 2 N6 ? ? ? 1_555 B A 1 N7 ? ? A A 2 B A 12 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog2 hydrog ? ? A A 2 N7 ? ? ? 1_555 B A 1 N6 ? ? A A 2 B A 12 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog3 hydrog ? ? A A 3 N6 ? ? ? 1_555 B A 2 N7 ? ? A A 3 B A 13 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog4 hydrog ? ? A A 3 N7 ? ? ? 1_555 B A 2 N6 ? ? A A 3 B A 13 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog5 hydrog ? ? A A 4 N6 ? ? ? 1_555 B A 3 N7 ? ? A A 4 B A 14 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog6 hydrog ? ? A A 4 N7 ? ? ? 1_555 B A 3 N6 ? ? A A 4 B A 14 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog7 hydrog ? ? A A 5 N6 ? ? ? 1_555 B A 4 N7 ? ? A A 5 B A 15 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog8 hydrog ? ? A A 5 N7 ? ? ? 1_555 B A 4 N6 ? ? A A 5 B A 15 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog9 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B A 5 N7 ? ? A DA 6 B A 16 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog10 hydrog ? ? A DA 6 N7 ? ? ? 1_555 B A 5 N6 ? ? A DA 6 B A 16 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog11 hydrog ? ? A A 7 N6 ? ? ? 1_555 B DA 6 N7 ? ? A A 7 B DA 17 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog12 hydrog ? ? A A 7 N7 ? ? ? 1_555 B DA 6 N6 ? ? A A 7 B DA 17 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog13 hydrog ? ? A A 8 N6 ? ? ? 1_555 B A 7 N7 ? ? A A 8 B A 18 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog14 hydrog ? ? A A 8 N7 ? ? ? 1_555 B A 7 N6 ? ? A A 8 B A 18 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog15 hydrog ? ? A A 9 N6 ? ? ? 1_555 B A 8 N7 ? ? A A 9 B A 19 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog16 hydrog ? ? A A 9 N7 ? ? ? 1_555 B A 8 N6 ? ? A A 9 B A 19 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog17 hydrog ? ? A A 10 N6 ? ? ? 1_555 B A 9 N7 ? ? A A 10 B A 20 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog18 hydrog ? ? A A 10 N7 ? ? ? 1_555 B A 9 N6 ? ? A A 10 B A 20 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog19 hydrog ? ? A A 11 N6 ? ? ? 1_555 B A 10 N7 ? ? A A 11 B A 21 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? hydrog20 hydrog ? ? A A 11 N7 ? ? ? 1_555 B A 10 N6 ? ? A A 11 B A 21 1_555 ? ? ? ? ? ? TYPE_2_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 A NH4 101 ? 6 'binding site for residue NH4 A 101' AC2 Software A NH4 102 ? 3 'binding site for residue NH4 A 102' AC3 Software A NH4 103 ? 4 'binding site for residue NH4 A 103' AC4 Software A NH4 104 ? 5 'binding site for residue NH4 A 104' AC5 Software A NH4 105 ? 5 'binding site for residue NH4 A 105' AC6 Software A NH4 106 ? 4 'binding site for residue NH4 A 106' AC7 Software A NH4 107 ? 4 'binding site for residue NH4 A 107' AC8 Software A NH4 108 ? 4 'binding site for residue NH4 A 108' AC9 Software A NH4 109 ? 5 'binding site for residue NH4 A 109' AD1 Software A NH4 110 ? 5 'binding site for residue NH4 A 110' AD2 Software A NH4 111 ? 4 'binding site for residue NH4 A 111' AD3 Software A NH4 112 ? 6 'binding site for residue NH4 A 112' AD4 Software B NH4 101 ? 4 'binding site for residue NH4 B 101' AD5 Software B NH4 102 ? 4 'binding site for residue NH4 B 102' AD6 Software B NH4 103 ? 6 'binding site for residue NH4 B 103' AD7 Software B NH4 104 ? 6 'binding site for residue NH4 B 104' AD8 Software B NH4 105 ? 5 'binding site for residue NH4 B 105' AD9 Software B NH4 106 ? 4 'binding site for residue NH4 B 106' # 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 6 A A 5 ? A A 5 . ? 1_555 ? 2 AC1 6 DA A 6 ? DA A 6 . ? 1_555 ? 3 AC1 6 A A 9 ? A A 9 . ? 7_655 ? 4 AC1 6 NH4 G . ? NH4 A 105 . ? 7_655 ? 5 AC1 6 A B 5 ? A B 16 . ? 1_555 ? 6 AC1 6 DA B 6 ? DA B 17 . ? 1_555 ? 7 AC2 3 A A 2 ? A A 2 . ? 1_555 ? 8 AC2 3 A A 3 ? A A 3 . ? 1_555 ? 9 AC2 3 A B 2 ? A B 13 . ? 1_555 ? 10 AC3 4 A A 3 ? A A 3 . ? 1_555 ? 11 AC3 4 A A 4 ? A A 4 . ? 1_555 ? 12 AC3 4 A A 11 ? A A 11 . ? 7_645 ? 13 AC3 4 A B 3 ? A B 14 . ? 1_555 ? 14 AC4 5 DA A 6 ? DA A 6 . ? 1_555 ? 15 AC4 5 A A 7 ? A A 7 . ? 1_555 ? 16 AC4 5 HOH U . ? HOH A 206 . ? 7_655 ? 17 AC4 5 HOH U . ? HOH A 219 . ? 1_555 ? 18 AC4 5 DA B 6 ? DA B 17 . ? 1_555 ? 19 AC5 5 A A 5 ? A A 5 . ? 7_545 ? 20 AC5 5 A A 9 ? A A 9 . ? 1_555 ? 21 AC5 5 A A 10 ? A A 10 . ? 1_555 ? 22 AC5 5 NH4 C . ? NH4 A 101 . ? 7_545 ? 23 AC5 5 A B 9 ? A B 20 . ? 1_555 ? 24 AC6 4 A A 4 ? A A 4 . ? 7_545 ? 25 AC6 4 A A 10 ? A A 10 . ? 1_555 ? 26 AC6 4 A A 11 ? A A 11 . ? 1_555 ? 27 AC6 4 A B 10 ? A B 21 . ? 1_555 ? 28 AC7 4 A A 7 ? A A 7 . ? 1_555 ? 29 AC7 4 A A 8 ? A A 8 . ? 1_555 ? 30 AC7 4 HOH U . ? HOH A 214 . ? 7_555 ? 31 AC7 4 A B 7 ? A B 18 . ? 1_555 ? 32 AC8 4 A A 8 ? A A 8 . ? 1_555 ? 33 AC8 4 A A 9 ? A A 9 . ? 1_555 ? 34 AC8 4 HOH U . ? HOH A 222 . ? 1_555 ? 35 AC8 4 A B 8 ? A B 19 . ? 1_555 ? 36 AC9 5 A A 4 ? A A 4 . ? 1_555 ? 37 AC9 5 A A 5 ? A A 5 . ? 1_555 ? 38 AC9 5 HOH U . ? HOH A 226 . ? 1_555 ? 39 AC9 5 A B 4 ? A B 15 . ? 1_555 ? 40 AC9 5 A B 5 ? A B 16 . ? 1_555 ? 41 AD1 5 A A 7 ? A A 7 . ? 1_555 ? 42 AD1 5 A A 8 ? A A 8 . ? 1_555 ? 43 AD1 5 HOH U . ? HOH A 220 . ? 1_555 ? 44 AD1 5 A B 5 ? A B 16 . ? 1_555 ? 45 AD1 5 DA B 6 ? DA B 17 . ? 1_555 ? 46 AD2 4 A A 10 ? A A 10 . ? 1_555 ? 47 AD2 4 A A 11 ? A A 11 . ? 1_555 ? 48 AD2 4 A B 8 ? A B 19 . ? 1_555 ? 49 AD2 4 A B 9 ? A B 20 . ? 1_555 ? 50 AD3 6 A A 8 ? A A 8 . ? 1_555 ? 51 AD3 6 A A 9 ? A A 9 . ? 1_555 ? 52 AD3 6 HOH U . ? HOH A 238 . ? 7_645 ? 53 AD3 6 DA B 6 ? DA B 17 . ? 7_645 ? 54 AD3 6 DA B 6 ? DA B 17 . ? 1_555 ? 55 AD3 6 A B 7 ? A B 18 . ? 1_555 ? 56 AD4 4 A A 1 ? A A 1 . ? 3_645 ? 57 AD4 4 A A 11 ? A A 11 . ? 1_555 ? 58 AD4 4 A B 9 ? A B 20 . ? 1_555 ? 59 AD4 4 A B 10 ? A B 21 . ? 1_555 ? 60 AD5 4 A A 3 ? A A 3 . ? 1_555 ? 61 AD5 4 A B 1 ? A B 12 . ? 1_555 ? 62 AD5 4 A B 2 ? A B 13 . ? 1_555 ? 63 AD5 4 HOH V . ? HOH B 210 . ? 1_555 ? 64 AD6 6 A A 9 ? A A 9 . ? 1_555 ? 65 AD6 6 A A 10 ? A A 10 . ? 1_555 ? 66 AD6 6 A B 5 ? A B 16 . ? 7_645 ? 67 AD6 6 A B 7 ? A B 18 . ? 1_555 ? 68 AD6 6 A B 8 ? A B 19 . ? 1_555 ? 69 AD6 6 HOH V . ? HOH B 207 . ? 7_645 ? 70 AD7 6 A A 4 ? A A 4 . ? 1_555 ? 71 AD7 6 A A 5 ? A A 5 . ? 1_555 ? 72 AD7 6 A B 2 ? A B 13 . ? 1_555 ? 73 AD7 6 A B 3 ? A B 14 . ? 1_555 ? 74 AD7 6 HOH V . ? HOH B 223 . ? 7_555 ? 75 AD7 6 HOH V . ? HOH B 225 . ? 1_555 ? 76 AD8 5 DA A 6 ? DA A 6 . ? 1_555 ? 77 AD8 5 A A 7 ? A A 7 . ? 1_555 ? 78 AD8 5 A B 4 ? A B 15 . ? 1_555 ? 79 AD8 5 A B 5 ? A B 16 . ? 1_555 ? 80 AD8 5 HOH V . ? HOH B 214 . ? 7_545 ? 81 AD9 4 A A 5 ? A A 5 . ? 1_555 ? 82 AD9 4 DA A 6 ? DA A 6 . ? 1_555 ? 83 AD9 4 A B 3 ? A B 14 . ? 1_555 ? 84 AD9 4 A B 4 ? A B 15 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 219 ? ? O A HOH 225 ? ? 2.10 2 1 O B HOH 201 ? ? O B HOH 213 ? ? 2.13 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 N6 A A 8 ? ? 1_555 O A HOH 238 ? ? 7_645 2.16 2 1 "O5'" B DA 17 ? ? 1_555 O A HOH 238 ? ? 7_645 2.17 # _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 228 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id U _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 DA OP3 O N N 38 DA P P N N 39 DA OP1 O N N 40 DA OP2 O N N 41 DA "O5'" O N N 42 DA "C5'" C N N 43 DA "C4'" C N R 44 DA "O4'" O N N 45 DA "C3'" C N S 46 DA "O3'" O N N 47 DA "C2'" C N N 48 DA "C1'" C N R 49 DA N9 N Y N 50 DA C8 C Y N 51 DA N7 N Y N 52 DA C5 C Y N 53 DA C6 C Y N 54 DA N6 N N N 55 DA N1 N Y N 56 DA C2 C Y N 57 DA N3 N Y N 58 DA C4 C Y N 59 DA HOP3 H N N 60 DA HOP2 H N N 61 DA "H5'" H N N 62 DA "H5''" H N N 63 DA "H4'" H N N 64 DA "H3'" H N N 65 DA "HO3'" H N N 66 DA "H2'" H N N 67 DA "H2''" H N N 68 DA "H1'" H N N 69 DA H8 H N N 70 DA H61 H N N 71 DA H62 H N N 72 DA H2 H N N 73 HOH O O N N 74 HOH H1 H N N 75 HOH H2 H N N 76 NH4 N N N N 77 NH4 HN1 H N N 78 NH4 HN2 H N N 79 NH4 HN3 H N N 80 NH4 HN4 H N N 81 # 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 DA OP3 P sing N N 40 DA OP3 HOP3 sing N N 41 DA P OP1 doub N N 42 DA P OP2 sing N N 43 DA P "O5'" sing N N 44 DA OP2 HOP2 sing N N 45 DA "O5'" "C5'" sing N N 46 DA "C5'" "C4'" sing N N 47 DA "C5'" "H5'" sing N N 48 DA "C5'" "H5''" sing N N 49 DA "C4'" "O4'" sing N N 50 DA "C4'" "C3'" sing N N 51 DA "C4'" "H4'" sing N N 52 DA "O4'" "C1'" sing N N 53 DA "C3'" "O3'" sing N N 54 DA "C3'" "C2'" sing N N 55 DA "C3'" "H3'" sing N N 56 DA "O3'" "HO3'" sing N N 57 DA "C2'" "C1'" sing N N 58 DA "C2'" "H2'" sing N N 59 DA "C2'" "H2''" sing N N 60 DA "C1'" N9 sing N N 61 DA "C1'" "H1'" sing N N 62 DA N9 C8 sing Y N 63 DA N9 C4 sing Y N 64 DA C8 N7 doub Y N 65 DA C8 H8 sing N N 66 DA N7 C5 sing Y N 67 DA C5 C6 sing Y N 68 DA C5 C4 doub Y N 69 DA C6 N6 sing N N 70 DA C6 N1 doub Y N 71 DA N6 H61 sing N N 72 DA N6 H62 sing N N 73 DA N1 C2 sing Y N 74 DA C2 N3 doub Y N 75 DA C2 H2 sing N N 76 DA N3 C4 sing Y N 77 HOH O H1 sing N N 78 HOH O H2 sing N N 79 NH4 N HN1 sing N N 80 NH4 N HN2 sing N N 81 NH4 N HN3 sing N N 82 NH4 N HN4 sing N N 83 # _ndb_struct_conf_na.entry_id 5VXQ _ndb_struct_conf_na.feature 'double 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 A 2 1_555 B A 1 1_555 6.214 -5.040 0.030 12.926 -3.954 179.512 1 A_A2:A12_B A 2 ? B 12 ? 2 8 1 A A 3 1_555 B A 2 1_555 6.139 -5.025 -0.433 10.616 -1.029 178.970 2 A_A3:A13_B A 3 ? B 13 ? 2 8 1 A A 4 1_555 B A 3 1_555 -6.207 5.012 0.042 -2.981 9.322 -179.920 3 A_A4:A14_B A 4 ? B 14 ? 2 8 1 A A 5 1_555 B A 4 1_555 6.163 -5.031 0.106 -0.427 -10.637 178.575 4 A_A5:A15_B A 5 ? B 15 ? 2 8 1 A DA 6 1_555 B A 5 1_555 -6.175 5.048 0.070 2.827 11.693 -179.785 5 A_DA6:A16_B A 6 ? B 16 ? 2 8 1 A A 7 1_555 B DA 6 1_555 -6.158 5.088 0.065 5.800 13.229 -176.506 6 A_A7:DA17_B A 7 ? B 17 ? 2 8 1 A A 8 1_555 B A 7 1_555 -6.024 5.156 -0.028 3.154 14.234 -179.813 7 A_A8:A18_B A 8 ? B 18 ? 2 8 1 A A 9 1_555 B A 8 1_555 6.070 -5.064 -0.051 -5.363 -15.295 178.545 8 A_A9:A19_B A 9 ? B 19 ? 2 8 1 A A 10 1_555 B A 9 1_555 -6.170 5.014 0.004 6.847 13.910 -179.699 9 A_A10:A20_B A 10 ? B 20 ? 2 8 1 A A 11 1_555 B A 10 1_555 -6.131 5.028 0.112 0.953 4.544 -179.152 10 A_A11:A21_B A 11 ? B 21 ? 2 8 # 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 A 2 1_555 B A 1 1_555 A A 3 1_555 B A 2 1_555 0.133 1.668 3.479 -6.241 -4.920 32.292 3.760 -1.302 3.119 -8.682 11.014 33.230 1 AA_A2A3:A13A12_BB A 2 ? B 12 ? A 3 ? B 13 ? 1 A A 3 1_555 B A 2 1_555 A A 4 1_555 B A 3 1_555 -0.115 0.513 3.854 0.469 4.905 -138.101 -0.308 -0.058 3.845 -2.626 0.251 -138.141 2 AA_A3A4:A14A13_BB A 3 ? B 13 ? A 4 ? B 14 ? 1 A A 4 1_555 B A 3 1_555 A A 5 1_555 B A 4 1_555 -0.457 -0.213 3.747 1.626 -0.950 -138.431 0.120 -0.234 3.748 0.508 0.870 -138.437 3 AA_A4A5:A15A14_BB A 4 ? B 14 ? A 5 ? B 15 ? 1 A A 5 1_555 B A 4 1_555 A DA 6 1_555 B A 5 1_555 0.212 -0.538 3.795 -2.037 1.005 -136.744 0.282 0.100 3.799 -0.540 -1.096 -136.753 4 AA_A5DA6:A16A15_BB A 5 ? B 15 ? A 6 ? B 16 ? 1 A DA 6 1_555 B A 5 1_555 A A 7 1_555 B DA 6 1_555 0.210 -0.425 3.773 -0.319 0.143 41.165 -0.623 -0.339 3.770 0.203 0.454 41.166 5 AA_DA6A7:DA17A16_BB A 6 ? B 16 ? A 7 ? B 17 ? 1 A A 7 1_555 B DA 6 1_555 A A 8 1_555 B A 7 1_555 -0.152 0.054 3.813 1.053 0.723 44.872 -0.006 0.311 3.809 0.947 -1.379 44.889 6 AA_A7A8:A18DA17_BB A 7 ? B 17 ? A 8 ? B 18 ? 1 A A 8 1_555 B A 7 1_555 A A 9 1_555 B A 8 1_555 -0.252 -0.035 3.835 0.858 -0.201 -138.222 0.020 -0.129 3.836 0.107 0.459 -138.224 7 AA_A8A9:A19A18_BB A 8 ? B 18 ? A 9 ? B 19 ? 1 A A 9 1_555 B A 8 1_555 A A 10 1_555 B A 9 1_555 -0.355 0.170 3.797 0.046 0.802 -138.222 -0.096 -0.190 3.797 -0.429 0.024 -138.223 8 AA_A9A10:A20A19_BB A 9 ? B 19 ? A 10 ? B 20 ? 1 A A 10 1_555 B A 9 1_555 A A 11 1_555 B A 10 1_555 -0.089 -0.062 3.555 -0.648 -1.102 39.370 0.049 0.049 3.557 -1.635 0.962 39.390 9 AA_A10A11:A21A20_BB A 10 ? B 20 ? A 11 ? B 21 ? # _atom_sites.entry_id 5VXQ _atom_sites.fract_transf_matrix[1][1] 0.043862 _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] 0.043862 _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] 0.006095 _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 C H N O P # loop_