data_5VBJ # _entry.id 5VBJ # _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 5VBJ pdb_00005vbj 10.2210/pdb5vbj/pdb WWPDB D_1000226914 ? ? # 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 2017-08-09 2 'Structure model' 1 1 2018-03-07 3 'Structure model' 1 2 2019-03-20 4 'Structure model' 1 3 2019-11-27 5 'Structure model' 1 4 2024-03-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 4 'Structure model' 'Author supporting evidence' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' # 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' diffrn_source 2 3 'Structure model' citation 3 3 'Structure model' citation_author 4 4 'Structure model' pdbx_audit_support 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 'Structure model' database_2 8 5 'Structure model' pdbx_struct_conn_angle 9 5 'Structure model' struct_conn # 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' '_diffrn_source.source' 2 3 'Structure model' '_citation.country' 3 3 'Structure model' '_citation.journal_abbrev' 4 3 'Structure model' '_citation.journal_id_CSD' 5 3 'Structure model' '_citation.journal_id_ISSN' 6 3 'Structure model' '_citation.journal_volume' 7 3 'Structure model' '_citation.page_first' 8 3 'Structure model' '_citation.page_last' 9 3 'Structure model' '_citation.pdbx_database_id_DOI' 10 3 'Structure model' '_citation.pdbx_database_id_PubMed' 11 3 'Structure model' '_citation.title' 12 3 'Structure model' '_citation.year' 13 4 'Structure model' '_pdbx_audit_support.funding_organization' 14 5 'Structure model' '_database_2.pdbx_DOI' 15 5 'Structure model' '_database_2.pdbx_database_accession' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 19 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 20 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 21 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 22 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 23 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 24 5 'Structure model' '_pdbx_struct_conn_angle.value' 25 5 'Structure model' '_struct_conn.pdbx_dist_value' 26 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 27 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 28 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 29 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 30 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 31 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 32 5 'Structure model' '_struct_conn.ptnr1_symmetry' 33 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 34 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 35 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 36 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 37 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 38 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 39 5 'Structure model' '_struct_conn.ptnr2_symmetry' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5VBJ _pdbx_database_status.recvd_initial_deposition_date 2017-03-29 _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 'Ford, M.C.' 1 ? 'Ho, P.S.' 2 ? # _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 Phys Chem Lett' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1948-7185 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 8 _citation.language ? _citation.page_first 4246 _citation.page_last 4252 _citation.title 'Sulfur as an Acceptor to Bromine in Biomolecular Halogen Bonds.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.jpclett.7b01725 _citation.pdbx_database_id_PubMed 28796521 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ford, M.C.' 1 0000-0002-0253-5389 primary 'Saxton, M.' 2 ? primary 'Ho, P.S.' 3 0000-0002-8082-4311 # 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 (5'-D(*CP*CP*GP*AP*TP*(AS)P*(BRU)P*CP*GP*G)-3') ; 3125.939 2 ? ? ? ? 2 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 3 water nat water 18.015 28 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DG)(DA)(DT)(AS)(BRU)(DC)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCGATAUCGG _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 'CALCIUM ION' CA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DG n 1 4 DA n 1 5 DT n 1 6 AS n 1 7 BRU n 1 8 DC n 1 9 DG n 1 10 DG 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 10 _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 AS 'DNA linking' n ;2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE ; ? 'C10 H14 N5 O5 P S' 347.287 BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DC 1 1 1 DC DC A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 AS 6 6 6 AS AS A . n A 1 7 BRU 7 7 7 BRU BRU A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DG 10 10 10 DG DG A . n B 1 1 DC 1 11 11 DC DC B . n B 1 2 DC 2 12 12 DC DC B . n B 1 3 DG 3 13 13 DG DG B . n B 1 4 DA 4 14 14 DA DA B . n B 1 5 DT 5 15 15 DT DT B . n B 1 6 AS 6 16 16 AS AS B . n B 1 7 BRU 7 17 17 BRU BRU B . n B 1 8 DC 8 18 18 DC DC B . n B 1 9 DG 9 19 19 DG DG B . n B 1 10 DG 10 20 20 DG DG 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 CA 1 101 29 CA CA B . D 3 HOH 1 101 3 HOH HOH A . D 3 HOH 2 102 9 HOH HOH A . D 3 HOH 3 103 11 HOH HOH A . D 3 HOH 4 104 23 HOH HOH A . D 3 HOH 5 105 14 HOH HOH A . D 3 HOH 6 106 13 HOH HOH A . D 3 HOH 7 107 24 HOH HOH A . D 3 HOH 8 108 28 HOH HOH A . D 3 HOH 9 109 17 HOH HOH A . D 3 HOH 10 110 5 HOH HOH A . D 3 HOH 11 111 12 HOH HOH A . D 3 HOH 12 112 26 HOH HOH A . D 3 HOH 13 113 27 HOH HOH A . D 3 HOH 14 114 7 HOH HOH A . D 3 HOH 15 115 18 HOH HOH A . D 3 HOH 16 116 22 HOH HOH A . E 3 HOH 1 201 15 HOH HOH B . E 3 HOH 2 202 2 HOH HOH B . E 3 HOH 3 203 10 HOH HOH B . E 3 HOH 4 204 21 HOH HOH B . E 3 HOH 5 205 19 HOH HOH B . E 3 HOH 6 206 1 HOH HOH B . E 3 HOH 7 207 8 HOH HOH B . E 3 HOH 8 208 4 HOH HOH B . E 3 HOH 9 209 6 HOH HOH B . E 3 HOH 10 210 16 HOH HOH B . E 3 HOH 11 211 20 HOH HOH B . E 3 HOH 12 212 25 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 ? ? ? 1.11.1_2575 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 112.32 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5VBJ _cell.details ? _cell.formula_units_Z ? _cell.length_a 64.165 _cell.length_a_esd ? _cell.length_b 23.981 _cell.length_b_esd ? _cell.length_c 37.815 _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 5VBJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' _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 5VBJ _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 2.15 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 42.86 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '25 mM sodium cacodylate, 15 mM calcium chloride, 1.0 mM spermine, and 0.75 mM DNA' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 200K' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-12-22 # _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 1.54 _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 'ROTATING ANODE' _diffrn_source.target ? _diffrn_source.type 'RIGAKU MICROMAX-003' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.54 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_synchrotron_site ? # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5VBJ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.94 _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 3562 _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 85.93 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.2 _reflns.pdbx_Rmerge_I_obs 0.088 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 12.4 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _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 . _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 5VBJ _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 1.944 _refine.ls_d_res_low 34.982 _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 5686 _refine.ls_number_reflns_R_free 563 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 74.07 _refine.ls_percent_reflns_R_free 9.90 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2240 _refine.ls_R_factor_R_free 0.2762 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2184 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.33 _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 ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 40.42 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.39 _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 404 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 28 _refine_hist.number_atoms_total 433 _refine_hist.d_res_high 1.944 _refine_hist.d_res_low 34.982 # 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' ? 0.009 ? 484 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.197 ? 735 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 37.852 ? 174 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.053 ? 80 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.007 ? 22 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.9443 2.1400 . . 71 697 40.00 . . . 0.4219 . 0.4177 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.1400 2.4496 . . 139 1220 72.00 . . . 0.4142 . 0.3542 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.4496 3.0859 . . 171 1534 89.00 . . . 0.3227 . 0.3004 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0859 34.9879 . . 182 1672 97.00 . . . 0.2197 . 0.1553 . . . . . . . . . . # _struct.entry_id 5VBJ _struct.title 'Sulfur as a bromine biomolecular halogen-bond acceptor' _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 5VBJ _struct_keywords.text 'Biophysics, Bromine, DNA, Sulfur, Halogen Bonding, Models, Molecular, Molecular Conformation, Uracil' _struct_keywords.pdbx_keywords 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 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5VBJ _struct_ref.pdbx_db_accession 5VBJ _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 5VBJ A 1 ? 10 ? 5VBJ 1 ? 10 ? 1 10 2 1 5VBJ B 1 ? 10 ? 5VBJ 11 ? 20 ? 11 20 # _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 # 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)' 6580 ? 1 MORE 1 ? 1 'SSA (A^2)' 5880 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_556 -x,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 -14.3613464972 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 34.9817945764 # 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 DT 5 "O3'" A ? ? 1_555 A AS 6 P A ? A DT 5 A AS 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale both ? A DT 5 "O3'" B ? ? 1_555 A AS 6 P B ? A DT 5 A AS 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? A AS 6 "O3'" A ? ? 1_555 A BRU 7 P ? ? A AS 6 A BRU 7 1_555 ? ? ? ? ? ? ? 1.559 ? ? covale4 covale both ? A AS 6 "O3'" B ? ? 1_555 A BRU 7 P ? ? A AS 6 A BRU 7 1_555 ? ? ? ? ? ? ? 1.559 ? ? covale5 covale both ? A BRU 7 "O3'" ? ? ? 1_555 A DC 8 P ? ? A BRU 7 A DC 8 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale6 covale both ? B DT 5 "O3'" ? ? ? 1_555 B AS 6 P ? ? B DT 15 B AS 16 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale7 covale both ? B AS 6 "O3'" ? ? ? 1_555 B BRU 7 P ? ? B AS 16 B BRU 17 1_555 ? ? ? ? ? ? ? 1.558 ? ? covale8 covale both ? B BRU 7 "O3'" ? ? ? 1_555 B DC 8 P ? ? B BRU 17 B DC 18 1_555 ? ? ? ? ? ? ? 1.604 ? ? metalc1 metalc ? ? D HOH . O ? ? ? 2_556 C CA . CA ? ? A HOH 105 B CA 101 1_555 ? ? ? ? ? ? ? 2.625 ? ? metalc2 metalc ? ? D HOH . O ? ? ? 2_556 C CA . CA ? ? A HOH 111 B CA 101 1_555 ? ? ? ? ? ? ? 2.636 ? ? metalc3 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? B CA 101 B HOH 202 1_555 ? ? ? ? ? ? ? 2.614 ? ? metalc4 metalc ? ? C CA . CA ? ? ? 1_555 E HOH . O ? ? B CA 101 B HOH 206 1_555 ? ? ? ? ? ? ? 2.608 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B BRU 7 N3 ? ? A DA 4 B BRU 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B BRU 7 O4 ? ? A DA 4 B BRU 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 A ? ? 1_555 B AS 6 N1 ? ? A DT 5 B AS 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 N3 B ? ? 1_555 B AS 6 N1 ? ? A DT 5 B AS 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 5 O4 A ? ? 1_555 B AS 6 N6 ? ? A DT 5 B AS 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 5 O4 B ? ? 1_555 B AS 6 N6 ? ? A DT 5 B AS 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A AS 6 N1 ? ? ? 1_555 B DT 5 N3 ? ? A AS 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A AS 6 N6 ? ? ? 1_555 B DT 5 O4 ? ? A AS 6 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 105 ? 2_556 CA ? C CA . ? B CA 101 ? 1_555 O ? D HOH . ? A HOH 111 ? 2_556 62.4 ? 2 O ? D HOH . ? A HOH 105 ? 2_556 CA ? C CA . ? B CA 101 ? 1_555 O ? E HOH . ? B HOH 202 ? 1_555 81.9 ? 3 O ? D HOH . ? A HOH 111 ? 2_556 CA ? C CA . ? B CA 101 ? 1_555 O ? E HOH . ? B HOH 202 ? 1_555 101.1 ? 4 O ? D HOH . ? A HOH 105 ? 2_556 CA ? C CA . ? B CA 101 ? 1_555 O ? E HOH . ? B HOH 206 ? 1_555 112.8 ? 5 O ? D HOH . ? A HOH 111 ? 2_556 CA ? C CA . ? B CA 101 ? 1_555 O ? E HOH . ? B HOH 206 ? 1_555 67.7 ? 6 O ? E HOH . ? B HOH 202 ? 1_555 CA ? C CA . ? B CA 101 ? 1_555 O ? E HOH . ? B HOH 206 ? 1_555 66.5 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id CA _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'binding site for residue CA B 101' # 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 4 HOH D . ? HOH A 105 . ? 2_556 ? 2 AC1 4 HOH D . ? HOH A 111 . ? 2_556 ? 3 AC1 4 HOH E . ? HOH B 202 . ? 1_555 ? 4 AC1 4 HOH E . ? HOH B 206 . ? 1_555 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DG _pdbx_validate_rmsd_bond.auth_seq_id_1 13 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DG _pdbx_validate_rmsd_bond.auth_seq_id_2 13 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.368 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.051 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DT 5 ? B "C1'" A DT 5 ? B N1 A DT 5 ? B 110.18 108.30 1.88 0.30 N 2 1 "C3'" A AS 6 ? A "O3'" A AS 6 ? A P A BRU 7 ? ? 126.94 119.70 7.24 1.20 Y 3 1 "O3'" A AS 6 ? B P A BRU 7 ? ? "O5'" A BRU 7 ? ? 117.35 104.00 13.35 1.90 Y 4 1 "C3'" B AS 16 ? ? "O3'" B AS 16 ? ? P B BRU 17 ? ? 101.31 119.70 -18.39 1.20 Y 5 1 "O3'" B AS 16 ? ? P B BRU 17 ? ? OP2 B BRU 17 ? ? 130.50 110.50 20.00 1.10 Y # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 106 ? D HOH . 2 1 B HOH 212 ? E HOH . # 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 AS P P N N 1 AS OP1 O N N 2 AS S2P S N N 3 AS OP3 O N N 4 AS "O5'" O N N 5 AS "C5'" C N N 6 AS "C4'" C N R 7 AS "O4'" O N N 8 AS "C3'" C N S 9 AS "O3'" O N N 10 AS "C2'" C N N 11 AS "C1'" C N R 12 AS N9 N Y N 13 AS C8 C Y N 14 AS N7 N Y N 15 AS C5 C Y N 16 AS C6 C Y N 17 AS N6 N N N 18 AS N1 N Y N 19 AS C2 C Y N 20 AS N3 N Y N 21 AS C4 C Y N 22 AS HOP1 H N N 23 AS HOP3 H N N 24 AS "H5'" H N N 25 AS "H5''" H N N 26 AS "H4'" H N N 27 AS "H3'" H N N 28 AS "HO3'" H N N 29 AS "H2'" H N N 30 AS "H2''" H N N 31 AS "H1'" H N N 32 AS H8 H N N 33 AS HN61 H N N 34 AS HN62 H N N 35 AS H2 H N N 36 BRU N1 N N N 37 BRU C2 C N N 38 BRU N3 N N N 39 BRU C4 C N N 40 BRU C5 C N N 41 BRU C6 C N N 42 BRU O2 O N N 43 BRU O4 O N N 44 BRU BR BR N N 45 BRU "C1'" C N R 46 BRU "C2'" C N N 47 BRU "C3'" C N S 48 BRU "C4'" C N R 49 BRU "O3'" O N N 50 BRU "O4'" O N N 51 BRU "C5'" C N N 52 BRU "O5'" O N N 53 BRU P P N N 54 BRU OP1 O N N 55 BRU OP2 O N N 56 BRU OP3 O N N 57 BRU HN3 H N N 58 BRU H6 H N N 59 BRU "H1'" H N N 60 BRU "H2'" H N N 61 BRU "H2''" H N N 62 BRU "H3'" H N N 63 BRU "H4'" H N N 64 BRU "HO3'" H N N 65 BRU "H5'" H N N 66 BRU "H5''" H N N 67 BRU HOP2 H N N 68 BRU HOP3 H N N 69 CA CA CA N N 70 DA OP3 O N N 71 DA P P N N 72 DA OP1 O N N 73 DA OP2 O N N 74 DA "O5'" O N N 75 DA "C5'" C N N 76 DA "C4'" C N R 77 DA "O4'" O N N 78 DA "C3'" C N S 79 DA "O3'" O N N 80 DA "C2'" C N N 81 DA "C1'" C N R 82 DA N9 N Y N 83 DA C8 C Y N 84 DA N7 N Y N 85 DA C5 C Y N 86 DA C6 C Y N 87 DA N6 N N N 88 DA N1 N Y N 89 DA C2 C Y N 90 DA N3 N Y N 91 DA C4 C Y N 92 DA HOP3 H N N 93 DA HOP2 H N N 94 DA "H5'" H N N 95 DA "H5''" H N N 96 DA "H4'" H N N 97 DA "H3'" H N N 98 DA "HO3'" H N N 99 DA "H2'" H N N 100 DA "H2''" H N N 101 DA "H1'" H N N 102 DA H8 H N N 103 DA H61 H N N 104 DA H62 H N N 105 DA H2 H N N 106 DC OP3 O N N 107 DC P P N N 108 DC OP1 O N N 109 DC OP2 O N N 110 DC "O5'" O N N 111 DC "C5'" C N N 112 DC "C4'" C N R 113 DC "O4'" O N N 114 DC "C3'" C N S 115 DC "O3'" O N N 116 DC "C2'" C N N 117 DC "C1'" C N R 118 DC N1 N N N 119 DC C2 C N N 120 DC O2 O N N 121 DC N3 N N N 122 DC C4 C N N 123 DC N4 N N N 124 DC C5 C N N 125 DC C6 C N N 126 DC HOP3 H N N 127 DC HOP2 H N N 128 DC "H5'" H N N 129 DC "H5''" H N N 130 DC "H4'" H N N 131 DC "H3'" H N N 132 DC "HO3'" H N N 133 DC "H2'" H N N 134 DC "H2''" H N N 135 DC "H1'" H N N 136 DC H41 H N N 137 DC H42 H N N 138 DC H5 H N N 139 DC H6 H N N 140 DG OP3 O N N 141 DG P P N N 142 DG OP1 O N N 143 DG OP2 O N N 144 DG "O5'" O N N 145 DG "C5'" C N N 146 DG "C4'" C N R 147 DG "O4'" O N N 148 DG "C3'" C N S 149 DG "O3'" O N N 150 DG "C2'" C N N 151 DG "C1'" C N R 152 DG N9 N Y N 153 DG C8 C Y N 154 DG N7 N Y N 155 DG C5 C Y N 156 DG C6 C N N 157 DG O6 O N N 158 DG N1 N N N 159 DG C2 C N N 160 DG N2 N N N 161 DG N3 N N N 162 DG C4 C Y N 163 DG HOP3 H N N 164 DG HOP2 H N N 165 DG "H5'" H N N 166 DG "H5''" H N N 167 DG "H4'" H N N 168 DG "H3'" H N N 169 DG "HO3'" H N N 170 DG "H2'" H N N 171 DG "H2''" H N N 172 DG "H1'" H N N 173 DG H8 H N N 174 DG H1 H N N 175 DG H21 H N N 176 DG H22 H N N 177 DT OP3 O N N 178 DT P P N N 179 DT OP1 O N N 180 DT OP2 O N N 181 DT "O5'" O N N 182 DT "C5'" C N N 183 DT "C4'" C N R 184 DT "O4'" O N N 185 DT "C3'" C N S 186 DT "O3'" O N N 187 DT "C2'" C N N 188 DT "C1'" C N R 189 DT N1 N N N 190 DT C2 C N N 191 DT O2 O N N 192 DT N3 N N N 193 DT C4 C N N 194 DT O4 O N N 195 DT C5 C N N 196 DT C7 C N N 197 DT C6 C N N 198 DT HOP3 H N N 199 DT HOP2 H N N 200 DT "H5'" H N N 201 DT "H5''" H N N 202 DT "H4'" H N N 203 DT "H3'" H N N 204 DT "HO3'" H N N 205 DT "H2'" H N N 206 DT "H2''" H N N 207 DT "H1'" H N N 208 DT H3 H N N 209 DT H71 H N N 210 DT H72 H N N 211 DT H73 H N N 212 DT H6 H N N 213 HOH O O N N 214 HOH H1 H N N 215 HOH H2 H N N 216 # 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 AS P OP1 sing N N 1 AS P S2P doub N N 2 AS P OP3 sing N N 3 AS P "O5'" sing N N 4 AS OP1 HOP1 sing N N 5 AS OP3 HOP3 sing N N 6 AS "O5'" "C5'" sing N N 7 AS "C5'" "C4'" sing N N 8 AS "C5'" "H5'" sing N N 9 AS "C5'" "H5''" sing N N 10 AS "C4'" "O4'" sing N N 11 AS "C4'" "C3'" sing N N 12 AS "C4'" "H4'" sing N N 13 AS "O4'" "C1'" sing N N 14 AS "C3'" "O3'" sing N N 15 AS "C3'" "C2'" sing N N 16 AS "C3'" "H3'" sing N N 17 AS "O3'" "HO3'" sing N N 18 AS "C2'" "C1'" sing N N 19 AS "C2'" "H2'" sing N N 20 AS "C2'" "H2''" sing N N 21 AS "C1'" N9 sing N N 22 AS "C1'" "H1'" sing N N 23 AS N9 C8 sing Y N 24 AS N9 C4 sing Y N 25 AS C8 N7 doub Y N 26 AS C8 H8 sing N N 27 AS N7 C5 sing Y N 28 AS C5 C6 sing Y N 29 AS C5 C4 doub Y N 30 AS C6 N6 sing N N 31 AS C6 N1 doub Y N 32 AS N6 HN61 sing N N 33 AS N6 HN62 sing N N 34 AS N1 C2 sing Y N 35 AS C2 N3 doub Y N 36 AS C2 H2 sing N N 37 AS N3 C4 sing Y N 38 BRU N1 C2 sing N N 39 BRU N1 C6 sing N N 40 BRU N1 "C1'" sing N N 41 BRU C2 N3 sing N N 42 BRU C2 O2 doub N N 43 BRU N3 C4 sing N N 44 BRU N3 HN3 sing N N 45 BRU C4 C5 sing N N 46 BRU C4 O4 doub N N 47 BRU C5 C6 doub N N 48 BRU C5 BR sing N N 49 BRU C6 H6 sing N N 50 BRU "C1'" "C2'" sing N N 51 BRU "C1'" "O4'" sing N N 52 BRU "C1'" "H1'" sing N N 53 BRU "C2'" "C3'" sing N N 54 BRU "C2'" "H2'" sing N N 55 BRU "C2'" "H2''" sing N N 56 BRU "C3'" "C4'" sing N N 57 BRU "C3'" "O3'" sing N N 58 BRU "C3'" "H3'" sing N N 59 BRU "C4'" "O4'" sing N N 60 BRU "C4'" "C5'" sing N N 61 BRU "C4'" "H4'" sing N N 62 BRU "O3'" "HO3'" sing N N 63 BRU "C5'" "O5'" sing N N 64 BRU "C5'" "H5'" sing N N 65 BRU "C5'" "H5''" sing N N 66 BRU "O5'" P sing N N 67 BRU P OP1 doub N N 68 BRU P OP2 sing N N 69 BRU P OP3 sing N N 70 BRU OP2 HOP2 sing N N 71 BRU OP3 HOP3 sing N N 72 DA OP3 P sing N N 73 DA OP3 HOP3 sing N N 74 DA P OP1 doub N N 75 DA P OP2 sing N N 76 DA P "O5'" sing N N 77 DA OP2 HOP2 sing N N 78 DA "O5'" "C5'" sing N N 79 DA "C5'" "C4'" sing N N 80 DA "C5'" "H5'" sing N N 81 DA "C5'" "H5''" sing N N 82 DA "C4'" "O4'" sing N N 83 DA "C4'" "C3'" sing N N 84 DA "C4'" "H4'" sing N N 85 DA "O4'" "C1'" sing N N 86 DA "C3'" "O3'" sing N N 87 DA "C3'" "C2'" sing N N 88 DA "C3'" "H3'" sing N N 89 DA "O3'" "HO3'" sing N N 90 DA "C2'" "C1'" sing N N 91 DA "C2'" "H2'" sing N N 92 DA "C2'" "H2''" sing N N 93 DA "C1'" N9 sing N N 94 DA "C1'" "H1'" sing N N 95 DA N9 C8 sing Y N 96 DA N9 C4 sing Y N 97 DA C8 N7 doub Y N 98 DA C8 H8 sing N N 99 DA N7 C5 sing Y N 100 DA C5 C6 sing Y N 101 DA C5 C4 doub Y N 102 DA C6 N6 sing N N 103 DA C6 N1 doub Y N 104 DA N6 H61 sing N N 105 DA N6 H62 sing N N 106 DA N1 C2 sing Y N 107 DA C2 N3 doub Y N 108 DA C2 H2 sing N N 109 DA N3 C4 sing Y N 110 DC OP3 P sing N N 111 DC OP3 HOP3 sing N N 112 DC P OP1 doub N N 113 DC P OP2 sing N N 114 DC P "O5'" sing N N 115 DC OP2 HOP2 sing N N 116 DC "O5'" "C5'" sing N N 117 DC "C5'" "C4'" sing N N 118 DC "C5'" "H5'" sing N N 119 DC "C5'" "H5''" sing N N 120 DC "C4'" "O4'" sing N N 121 DC "C4'" "C3'" sing N N 122 DC "C4'" "H4'" sing N N 123 DC "O4'" "C1'" sing N N 124 DC "C3'" "O3'" sing N N 125 DC "C3'" "C2'" sing N N 126 DC "C3'" "H3'" sing N N 127 DC "O3'" "HO3'" sing N N 128 DC "C2'" "C1'" sing N N 129 DC "C2'" "H2'" sing N N 130 DC "C2'" "H2''" sing N N 131 DC "C1'" N1 sing N N 132 DC "C1'" "H1'" sing N N 133 DC N1 C2 sing N N 134 DC N1 C6 sing N N 135 DC C2 O2 doub N N 136 DC C2 N3 sing N N 137 DC N3 C4 doub N N 138 DC C4 N4 sing N N 139 DC C4 C5 sing N N 140 DC N4 H41 sing N N 141 DC N4 H42 sing N N 142 DC C5 C6 doub N N 143 DC C5 H5 sing N N 144 DC C6 H6 sing N N 145 DG OP3 P sing N N 146 DG OP3 HOP3 sing N N 147 DG P OP1 doub N N 148 DG P OP2 sing N N 149 DG P "O5'" sing N N 150 DG OP2 HOP2 sing N N 151 DG "O5'" "C5'" sing N N 152 DG "C5'" "C4'" sing N N 153 DG "C5'" "H5'" sing N N 154 DG "C5'" "H5''" sing N N 155 DG "C4'" "O4'" sing N N 156 DG "C4'" "C3'" sing N N 157 DG "C4'" "H4'" sing N N 158 DG "O4'" "C1'" sing N N 159 DG "C3'" "O3'" sing N N 160 DG "C3'" "C2'" sing N N 161 DG "C3'" "H3'" sing N N 162 DG "O3'" "HO3'" sing N N 163 DG "C2'" "C1'" sing N N 164 DG "C2'" "H2'" sing N N 165 DG "C2'" "H2''" sing N N 166 DG "C1'" N9 sing N N 167 DG "C1'" "H1'" sing N N 168 DG N9 C8 sing Y N 169 DG N9 C4 sing Y N 170 DG C8 N7 doub Y N 171 DG C8 H8 sing N N 172 DG N7 C5 sing Y N 173 DG C5 C6 sing N N 174 DG C5 C4 doub Y N 175 DG C6 O6 doub N N 176 DG C6 N1 sing N N 177 DG N1 C2 sing N N 178 DG N1 H1 sing N N 179 DG C2 N2 sing N N 180 DG C2 N3 doub N N 181 DG N2 H21 sing N N 182 DG N2 H22 sing N N 183 DG N3 C4 sing N N 184 DT OP3 P sing N N 185 DT OP3 HOP3 sing N N 186 DT P OP1 doub N N 187 DT P OP2 sing N N 188 DT P "O5'" sing N N 189 DT OP2 HOP2 sing N N 190 DT "O5'" "C5'" sing N N 191 DT "C5'" "C4'" sing N N 192 DT "C5'" "H5'" sing N N 193 DT "C5'" "H5''" sing N N 194 DT "C4'" "O4'" sing N N 195 DT "C4'" "C3'" sing N N 196 DT "C4'" "H4'" sing N N 197 DT "O4'" "C1'" sing N N 198 DT "C3'" "O3'" sing N N 199 DT "C3'" "C2'" sing N N 200 DT "C3'" "H3'" sing N N 201 DT "O3'" "HO3'" sing N N 202 DT "C2'" "C1'" sing N N 203 DT "C2'" "H2'" sing N N 204 DT "C2'" "H2''" sing N N 205 DT "C1'" N1 sing N N 206 DT "C1'" "H1'" sing N N 207 DT N1 C2 sing N N 208 DT N1 C6 sing N N 209 DT C2 O2 doub N N 210 DT C2 N3 sing N N 211 DT N3 C4 sing N N 212 DT N3 H3 sing N N 213 DT C4 O4 doub N N 214 DT C4 C5 sing N N 215 DT C5 C7 sing N N 216 DT C5 C6 doub N N 217 DT C7 H71 sing N N 218 DT C7 H72 sing N N 219 DT C7 H73 sing N N 220 DT C6 H6 sing N N 221 HOH O H1 sing N N 222 HOH O H2 sing N N 223 # _ndb_struct_conf_na.entry_id 5VBJ _ndb_struct_conf_na.feature 'b-form 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 DC 1 1_555 B DG 10 1_555 0.343 -0.032 0.181 -2.227 -12.753 0.319 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.189 -0.585 0.219 6.402 -6.833 1.693 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 0.170 -0.166 0.540 5.841 -14.018 -0.479 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DA 4 1_555 B BRU 7 1_555 0.022 -0.026 0.171 -4.854 -15.369 3.375 4 A_DA4:BRU17_B A 4 ? B 17 ? 20 1 1 A DT 5 1_555 B AS 6 1_555 -0.915 0.114 0.501 -17.122 -18.694 3.975 5 A_DT5:AS16_B A 5 ? B 16 ? 20 1 1 A AS 6 1_555 B DT 5 1_555 0.470 -0.222 0.089 -0.593 -13.025 2.520 6 A_AS6:DT15_B A 6 ? B 15 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.581 1.856 3.275 4.694 2.004 37.212 2.615 -0.274 3.412 3.123 -7.314 37.549 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 -0.778 0.914 3.406 -6.666 1.463 38.826 1.172 0.312 3.518 2.180 9.934 39.399 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DA 4 1_555 B BRU 7 1_555 0.016 -0.205 3.449 1.139 -2.338 38.337 -0.003 0.125 3.454 -3.556 -1.732 38.422 3 AA_DG3DA4:BRU17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 4 1_555 B BRU 7 1_555 A DT 5 1_555 B AS 6 1_555 -0.448 -0.698 3.471 -3.286 -2.893 30.568 -0.705 0.153 3.548 -5.452 6.192 30.872 4 AA_DA4DT5:AS16BRU17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B AS 6 1_555 A AS 6 1_555 B DT 5 1_555 0.404 1.031 3.100 5.715 0.449 44.348 1.317 -0.032 3.136 0.592 -7.533 44.698 5 AA_DT5AS6:DT15AS16_BB A 5 ? B 16 ? A 6 ? B 15 ? # _pdbx_audit_support.funding_organization 'National Science Foundation (NSF, United States)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 5351441 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 5VBJ _atom_sites.fract_transf_matrix[1][1] 0.015585 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006398 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041700 _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] 0.028586 _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 CA N O P S # loop_