data_5VJB # _entry.id 5VJB # _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 5VJB pdb_00005vjb 10.2210/pdb5vjb/pdb WWPDB D_1000227525 ? ? # 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 2017-06-28 2 'Structure model' 1 1 2017-08-30 3 'Structure model' 1 2 2017-09-13 4 'Structure model' 1 3 2020-01-01 5 'Structure model' 1 4 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 2 'Structure model' 'Refinement description' 3 3 'Structure model' 'Author supporting evidence' 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' citation 2 2 'Structure model' software 3 3 'Structure model' pdbx_audit_support 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' 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' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_software.name' 5 3 'Structure model' '_pdbx_audit_support.funding_organization' 6 4 'Structure model' '_pdbx_audit_support.funding_organization' 7 5 'Structure model' '_database_2.pdbx_DOI' 8 5 'Structure model' '_database_2.pdbx_database_accession' 9 5 'Structure model' '_struct_conn.conn_type_id' 10 5 'Structure model' '_struct_conn.id' 11 5 'Structure model' '_struct_conn.pdbx_dist_value' 12 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 13 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 14 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 15 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 16 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 17 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 18 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 19 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 20 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 21 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 22 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 23 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 24 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 25 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 26 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5VJB _pdbx_database_status.recvd_initial_deposition_date 2017-04-19 _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 ? # _pdbx_database_related.content_type unspecified _pdbx_database_related.db_id 5VJ9 _pdbx_database_related.db_name PDB _pdbx_database_related.details . # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Reiss, C.W.' 1 ? 'Strobel, S.A.' 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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev RNA _citation.journal_id_ASTM RNARFU _citation.journal_id_CSD 2122 _citation.journal_id_ISSN 1469-9001 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 23 _citation.language ? _citation.page_first 1338 _citation.page_last 1343 _citation.title 'Structural basis for ligand binding to the guanidine-II riboswitch.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1261/rna.061804.117 _citation.pdbx_database_id_PubMed 28600356 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Reiss, C.W.' 1 ? primary 'Strobel, S.A.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*GP*CP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*(5BU)P*GP*C)-3') ; 5246.047 4 ? ? ? ? 2 non-polymer syn GUANIDINE 59.070 4 ? ? ? ? 3 non-polymer syn SPERMINE 202.340 4 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 5 water nat water 18.015 11 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GCGGGGACGACCC(5BU)GC' _entity_poly.pdbx_seq_one_letter_code_can GCGGGGACGACCCUGC _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GUANIDINE GAI 3 SPERMINE SPM 4 'MAGNESIUM ION' MG 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 G n 1 4 G n 1 5 G n 1 6 G n 1 7 A n 1 8 C n 1 9 G n 1 10 A n 1 11 C n 1 12 C n 1 13 C n 1 14 5BU n 1 15 G n 1 16 C 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 16 _pdbx_entity_src_syn.organism_scientific 'Pseudomonas aeruginosa' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 287 _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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GAI non-polymer . GUANIDINE ? 'C H5 N3' 59.070 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 G 4 4 4 G G A . n A 1 5 G 5 5 5 G G A . n A 1 6 G 6 6 6 G G A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n A 1 9 G 9 9 9 G G A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 5BU 14 14 14 5BU 5BU A . n A 1 15 G 15 15 15 G G A . n A 1 16 C 16 16 16 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 G 3 3 3 G G B . n B 1 4 G 4 4 4 G G B . n B 1 5 G 5 5 5 G G B . n B 1 6 G 6 6 6 G G B . n B 1 7 A 7 7 7 A A B . n B 1 8 C 8 8 8 C C B . n B 1 9 G 9 9 9 G G B . n B 1 10 A 10 10 10 A A B . n B 1 11 C 11 11 11 C C B . n B 1 12 C 12 12 12 C C B . n B 1 13 C 13 13 13 C C B . n B 1 14 5BU 14 14 14 5BU 5BU B . n B 1 15 G 15 15 15 G G B . n B 1 16 C 16 16 16 C C B . n C 1 1 G 1 1 1 G G C . n C 1 2 C 2 2 2 C C C . n C 1 3 G 3 3 3 G G C . n C 1 4 G 4 4 4 G G C . n C 1 5 G 5 5 5 G G C . n C 1 6 G 6 6 6 G G C . n C 1 7 A 7 7 7 A A C . n C 1 8 C 8 8 8 C C C . n C 1 9 G 9 9 9 G G C . n C 1 10 A 10 10 10 A A C . n C 1 11 C 11 11 11 C C C . n C 1 12 C 12 12 12 C C C . n C 1 13 C 13 13 13 C C C . n C 1 14 5BU 14 14 14 5BU 5BU C . n C 1 15 G 15 15 15 G G C . n C 1 16 C 16 16 16 C C C . n D 1 1 G 1 1 1 G G D . n D 1 2 C 2 2 2 C C D . n D 1 3 G 3 3 3 G G D . n D 1 4 G 4 4 4 G G D . n D 1 5 G 5 5 5 G G D . n D 1 6 G 6 6 6 G G D . n D 1 7 A 7 7 7 A A D . n D 1 8 C 8 8 8 C C D . n D 1 9 G 9 9 9 G G D . n D 1 10 A 10 10 10 A A D . n D 1 11 C 11 11 11 C C D . n D 1 12 C 12 12 12 C C D . n D 1 13 C 13 13 13 C C D . n D 1 14 5BU 14 14 14 5BU 5BU D . n D 1 15 G 15 15 15 G G D . n D 1 16 C 16 16 16 C C D . 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 E 2 GAI 1 101 3 GAI GAI A . F 3 SPM 1 102 2 SPM SPM A . G 2 GAI 1 101 4 GAI GAI B . H 3 SPM 1 102 3 SPM SPM B . I 4 MG 1 103 1 MG MG B . J 2 GAI 1 101 2 GAI GAI C . K 3 SPM 1 102 4 SPM SPM C . L 2 GAI 1 101 1 GAI GAI D . M 3 SPM 1 102 1 SPM SPM D . N 5 HOH 1 201 1 HOH HOH A . N 5 HOH 2 202 6 HOH HOH A . O 5 HOH 1 201 8 HOH HOH B . O 5 HOH 2 202 7 HOH HOH B . O 5 HOH 3 203 10 HOH HOH B . O 5 HOH 4 204 11 HOH HOH B . O 5 HOH 5 205 9 HOH HOH B . P 5 HOH 1 201 4 HOH HOH C . Q 5 HOH 1 201 2 HOH HOH D . Q 5 HOH 2 202 3 HOH HOH D . Q 5 HOH 3 203 5 HOH HOH D . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0158 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALEPACK ? ? ? . 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELXDE ? ? ? . 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.22 4 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? . 5 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 6 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 5VJB _cell.details ? _cell.formula_units_Z ? _cell.length_a 50.234 _cell.length_a_esd ? _cell.length_b 60.540 _cell.length_b_esd ? _cell.length_c 71.914 _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 5VJB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _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 5VJB _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 2.61 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 52.79 _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 MICROBATCH _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.6 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 296.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;1:1 ratio of 200uM RNA in crystallization buffer (10 mM MgCl2, 10 mM KCl, 10 mM HEPES-KOH, pH 7.5, and 40 mM guanidine) and crystallization reagent (45% MPD, 50 mM MES, pH 5.6, 4 mM NaCl, 40 mM KCl, and 12 mM spermine) ; _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 6M-F' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-04-07 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.919300 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-C' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.919300 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-C _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5VJB _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.100 _reflns.d_resolution_low 40.000 _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 25445 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.900 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.800 _reflns.pdbx_Rmerge_I_obs 0.068 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 6.800 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.027 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.073 _reflns.pdbx_Rpim_I_all 0.028 _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 ? # loop_ _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 _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 2.100 2.140 ? ? ? ? ? ? ? 100.000 ? ? ? ? 1.058 ? ? ? ? ? ? ? ? 7.000 ? 0.820 ? ? 1.142 0.427 ? 1 1 0.552 ? 2.140 2.180 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.948 ? ? ? ? ? ? ? ? 6.900 ? 0.863 ? ? 1.024 0.384 ? 2 1 0.627 ? 2.180 2.220 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.916 ? ? ? ? ? ? ? ? 6.900 ? 0.858 ? ? 0.990 0.374 ? 3 1 0.637 ? 2.220 2.260 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.681 ? ? ? ? ? ? ? ? 6.800 ? 0.870 ? ? 0.737 0.280 ? 4 1 0.793 ? 2.260 2.310 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.568 ? ? ? ? ? ? ? ? 6.800 ? 0.894 ? ? 0.615 0.233 ? 5 1 0.848 ? 2.310 2.370 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.474 ? ? ? ? ? ? ? ? 6.800 ? 0.896 ? ? 0.513 0.195 ? 6 1 0.891 ? 2.370 2.420 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.404 ? ? ? ? ? ? ? ? 6.500 ? 0.938 ? ? 0.439 0.171 ? 7 1 0.907 ? 2.420 2.490 ? ? ? ? ? ? ? 99.800 ? ? ? ? 0.329 ? ? ? ? ? ? ? ? 6.100 ? 0.919 ? ? 0.360 0.145 ? 8 1 0.944 ? 2.490 2.560 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.286 ? ? ? ? ? ? ? ? 6.400 ? 0.910 ? ? 0.311 0.123 ? 9 1 0.956 ? 2.560 2.650 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.241 ? ? ? ? ? ? ? ? 7.100 ? 0.961 ? ? 0.260 0.097 ? 10 1 0.971 ? 2.650 2.740 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.190 ? ? ? ? ? ? ? ? 7.100 ? 0.940 ? ? 0.205 0.077 ? 11 1 0.984 ? 2.740 2.850 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.129 ? ? ? ? ? ? ? ? 7.000 ? 1.005 ? ? 0.139 0.053 ? 12 1 0.993 ? 2.850 2.980 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.101 ? ? ? ? ? ? ? ? 6.900 ? 1.119 ? ? 0.109 0.041 ? 13 1 0.997 ? 2.980 3.140 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.077 ? ? ? ? ? ? ? ? 6.600 ? 1.165 ? ? 0.084 0.032 ? 14 1 0.998 ? 3.140 3.330 ? ? ? ? ? ? ? 99.700 ? ? ? ? 0.061 ? ? ? ? ? ? ? ? 6.100 ? 1.307 ? ? 0.067 0.026 ? 15 1 0.999 ? 3.330 3.590 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.056 ? ? ? ? ? ? ? ? 7.300 ? 1.319 ? ? 0.061 0.023 ? 16 1 0.998 ? 3.590 3.950 ? ? ? ? ? ? ? 99.900 ? ? ? ? 0.048 ? ? ? ? ? ? ? ? 7.100 ? 1.257 ? ? 0.052 0.019 ? 17 1 0.999 ? 3.950 4.520 ? ? ? ? ? ? ? 100.000 ? ? ? ? 0.043 ? ? ? ? ? ? ? ? 6.900 ? 1.167 ? ? 0.047 0.018 ? 18 1 0.998 ? 4.520 5.700 ? ? ? ? ? ? ? 99.800 ? ? ? ? 0.037 ? ? ? ? ? ? ? ? 6.600 ? 1.114 ? ? 0.040 0.015 ? 19 1 0.999 ? 5.700 40.000 ? ? ? ? ? ? ? 99.800 ? ? ? ? 0.040 ? ? ? ? ? ? ? ? 6.900 ? 1.203 ? ? 0.043 0.017 ? 20 1 0.998 ? # _refine.aniso_B[1][1] 1.0200 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] -1.3800 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] 0.3600 _refine.B_iso_max 102.460 _refine.B_iso_mean 40.5340 _refine.B_iso_min 29.510 _refine.correlation_coeff_Fo_to_Fc 0.9630 _refine.correlation_coeff_Fo_to_Fc_free 0.9710 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY' _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 5VJB _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.1 _refine.ls_d_res_low 40 _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 13040 _refine.ls_number_reflns_R_free 634 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.3000 _refine.ls_percent_reflns_R_free 4.6000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2167 _refine.ls_R_factor_R_free 0.2383 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2156 _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 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.2050 _refine.pdbx_overall_ESU_R_Free 0.1680 _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _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 4.8440 _refine.overall_SU_ML 0.1270 _refine.overall_SU_R_Cruickshank_DPI 0.2048 _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.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 2.1 _refine_hist.d_res_low 40 _refine_hist.pdbx_number_atoms_ligand 73 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 1456 _refine_hist.pdbx_number_residues_total 64 _refine_hist.pdbx_B_iso_mean_ligand 60.01 _refine_hist.pdbx_B_iso_mean_solvent 36.09 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1372 # 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' ? 0.012 0.012 1601 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.008 0.020 761 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.995 1.393 2458 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.775 3.000 1797 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 0.106 0.200 256 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.017 0.020 824 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.003 0.020 396 ? r_gen_planes_other ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 2.0700 _refine_ls_shell.d_res_low 2.1240 _refine_ls_shell.number_reflns_all 793 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 36 _refine_ls_shell.number_reflns_R_work 757 _refine_ls_shell.percent_reflns_obs 78.0500 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.3910 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.3160 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 5VJB _struct.title 'Guanidine-II riboswitch P2 hairpin dimer with 5-bromoU substitution from Pseudomonas aeruginosa' _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 5VJB _struct_keywords.text 'guanidine, riboswitch, kissing loop, hairpin, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 3 ? G N N 2 ? H N N 3 ? I N N 4 ? J N N 2 ? K N N 3 ? L N N 2 ? M N N 3 ? N N N 5 ? O N N 5 ? P N N 5 ? Q N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5VJB _struct_ref.pdbx_db_accession 5VJB _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 5VJB A 1 ? 16 ? 5VJB 1 ? 16 ? 1 16 2 1 5VJB B 1 ? 16 ? 5VJB 1 ? 16 ? 1 16 3 1 5VJB C 1 ? 16 ? 5VJB 1 ? 16 ? 1 16 4 1 5VJB D 1 ? 16 ? 5VJB 1 ? 16 ? 1 16 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,E,F,G,H,I,N,O 2 1 C,D,J,K,L,M,P,Q # _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 ? # _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 covale1 covale both ? A C 13 "O3'" ? ? ? 1_555 A 5BU 14 P ? ? A C 13 A 5BU 14 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale2 covale both ? A 5BU 14 "O3'" ? ? ? 1_555 A G 15 P ? ? A 5BU 14 A G 15 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale3 covale both ? B C 13 "O3'" ? ? ? 1_555 B 5BU 14 P ? ? B C 13 B 5BU 14 1_555 ? ? ? ? ? ? ? 1.576 ? ? covale4 covale both ? B 5BU 14 "O3'" ? ? ? 1_555 B G 15 P ? ? B 5BU 14 B G 15 1_555 ? ? ? ? ? ? ? 1.631 ? ? covale5 covale both ? C C 13 "O3'" ? ? ? 1_555 C 5BU 14 P ? ? C C 13 C 5BU 14 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale6 covale both ? C 5BU 14 "O3'" ? ? ? 1_555 C G 15 P ? ? C 5BU 14 C G 15 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale7 covale both ? D C 13 "O3'" ? ? ? 1_555 D 5BU 14 P ? ? D C 13 D 5BU 14 1_555 ? ? ? ? ? ? ? 1.638 ? ? covale8 covale both ? D 5BU 14 "O3'" ? ? ? 1_555 D G 15 P ? ? D 5BU 14 D G 15 1_555 ? ? ? ? ? ? ? 1.624 ? ? metalc1 metalc ? ? B C 8 OP1 ? ? ? 1_555 I MG . MG ? ? B C 8 B MG 103 1_555 ? ? ? ? ? ? ? 2.188 ? ? metalc2 metalc ? ? I MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 103 B HOH 201 1_555 ? ? ? ? ? ? ? 2.157 ? ? metalc3 metalc ? ? I MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 103 B HOH 202 1_555 ? ? ? ? ? ? ? 2.184 ? ? metalc4 metalc ? ? I MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 103 B HOH 203 1_555 ? ? ? ? ? ? ? 2.147 ? ? metalc5 metalc ? ? I MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 103 B HOH 204 1_555 ? ? ? ? ? ? ? 2.154 ? ? metalc6 metalc ? ? I MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 103 B HOH 205 1_555 ? ? ? ? ? ? ? 2.201 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 1 A C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 2 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 2 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 2 A G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A 5BU 14 O2 ? ? A G 3 A 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog8 hydrog ? ? A G 3 O6 ? ? ? 1_555 A 5BU 14 N3 ? ? A G 3 A 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 12 N3 ? ? A G 5 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 5 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 5 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 6 A C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 6 A C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 6 A C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N6 ? ? ? 1_555 B C 11 O2 ? ? A A 7 B C 11 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog19 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 8 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 8 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 8 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 9 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 9 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 9 B C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 B A 7 N6 ? ? A C 11 B A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog26 hydrog ? ? B G 1 N1 ? ? ? 1_555 B C 16 N3 ? ? B G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B G 1 N2 ? ? ? 1_555 B C 16 O2 ? ? B G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B G 1 O6 ? ? ? 1_555 B C 16 N4 ? ? B G 1 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B C 2 N3 ? ? ? 1_555 B G 15 N1 ? ? B C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B C 2 N4 ? ? ? 1_555 B G 15 O6 ? ? B C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B C 2 O2 ? ? ? 1_555 B G 15 N2 ? ? B C 2 B G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B G 3 N1 ? ? ? 1_555 B 5BU 14 O2 ? ? B G 3 B 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog33 hydrog ? ? B G 3 O6 ? ? ? 1_555 B 5BU 14 N3 ? ? B G 3 B 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog34 hydrog ? ? B G 4 N1 ? ? ? 1_555 B C 13 N3 ? ? B G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 4 N2 ? ? ? 1_555 B C 13 O2 ? ? B G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B G 4 O6 ? ? ? 1_555 B C 13 N4 ? ? B G 4 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? B G 5 N1 ? ? ? 1_555 B C 12 N3 ? ? B G 5 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B G 5 N2 ? ? ? 1_555 B C 12 O2 ? ? B G 5 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B G 5 O6 ? ? ? 1_555 B C 12 N4 ? ? B G 5 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B G 6 N1 ? ? ? 1_555 B C 11 N3 ? ? B G 6 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B G 6 N2 ? ? ? 1_555 B C 11 O2 ? ? B G 6 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B G 6 O6 ? ? ? 1_555 B C 11 N4 ? ? B G 6 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C G 1 N1 ? ? ? 1_555 C C 16 N3 ? ? C G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C G 1 N2 ? ? ? 1_555 C C 16 O2 ? ? C G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C G 1 O6 ? ? ? 1_555 C C 16 N4 ? ? C G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C C 2 N3 ? ? ? 1_555 C G 15 N1 ? ? C C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C C 2 N4 ? ? ? 1_555 C G 15 O6 ? ? C C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C C 2 O2 ? ? ? 1_555 C G 15 N2 ? ? C C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C G 3 N1 ? ? ? 1_555 C 5BU 14 O2 ? ? C G 3 C 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog50 hydrog ? ? C G 3 O6 ? ? ? 1_555 C 5BU 14 N3 ? ? C G 3 C 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog51 hydrog ? ? C G 4 N1 ? ? ? 1_555 C C 13 N3 ? ? C G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? C G 4 N2 ? ? ? 1_555 C C 13 O2 ? ? C G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? C G 4 O6 ? ? ? 1_555 C C 13 N4 ? ? C G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? C G 5 N1 ? ? ? 1_555 C C 12 N3 ? ? C G 5 C C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? C G 5 N2 ? ? ? 1_555 C C 12 O2 ? ? C G 5 C C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? C G 5 O6 ? ? ? 1_555 C C 12 N4 ? ? C G 5 C C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? C G 6 N1 ? ? ? 1_555 C C 11 N3 ? ? C G 6 C C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? C G 6 N2 ? ? ? 1_555 C C 11 O2 ? ? C G 6 C C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? C G 6 O6 ? ? ? 1_555 C C 11 N4 ? ? C G 6 C C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? C A 7 N6 ? ? ? 1_555 D C 11 O2 ? ? C A 7 D C 11 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog61 hydrog ? ? C C 8 N3 ? ? ? 1_555 D G 9 N1 ? ? C C 8 D G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? C C 8 N4 ? ? ? 1_555 D G 9 O6 ? ? C C 8 D G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? C C 8 O2 ? ? ? 1_555 D G 9 N2 ? ? C C 8 D G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? C G 9 N1 ? ? ? 1_555 D C 8 N3 ? ? C G 9 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? C G 9 N2 ? ? ? 1_555 D C 8 O2 ? ? C G 9 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? C G 9 O6 ? ? ? 1_555 D C 8 N4 ? ? C G 9 D C 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? C C 11 O2 ? ? ? 1_555 D A 7 N6 ? ? C C 11 D A 7 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog68 hydrog ? ? D G 1 N1 ? ? ? 1_555 D C 16 N3 ? ? D G 1 D C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? D G 1 N2 ? ? ? 1_555 D C 16 O2 ? ? D G 1 D C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? D G 1 O6 ? ? ? 1_555 D C 16 N4 ? ? D G 1 D C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? D C 2 N3 ? ? ? 1_555 D G 15 N1 ? ? D C 2 D G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? D C 2 N4 ? ? ? 1_555 D G 15 O6 ? ? D C 2 D G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? D C 2 O2 ? ? ? 1_555 D G 15 N2 ? ? D C 2 D G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? D G 3 N1 ? ? ? 1_555 D 5BU 14 O2 ? ? D G 3 D 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog75 hydrog ? ? D G 3 O6 ? ? ? 1_555 D 5BU 14 N3 ? ? D G 3 D 5BU 14 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog76 hydrog ? ? D G 4 N1 ? ? ? 1_555 D C 13 N3 ? ? D G 4 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? D G 4 N2 ? ? ? 1_555 D C 13 O2 ? ? D G 4 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? D G 4 O6 ? ? ? 1_555 D C 13 N4 ? ? D G 4 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? D G 5 N1 ? ? ? 1_555 D C 12 N3 ? ? D G 5 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? D G 5 N2 ? ? ? 1_555 D C 12 O2 ? ? D G 5 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? D G 5 O6 ? ? ? 1_555 D C 12 N4 ? ? D G 5 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? D G 6 N1 ? ? ? 1_555 D C 11 N3 ? ? D G 6 D C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? D G 6 N2 ? ? ? 1_555 D C 11 O2 ? ? D G 6 D C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? D G 6 O6 ? ? ? 1_555 D C 11 N4 ? ? D G 6 D C 11 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 OP1 ? B C 8 ? B C 8 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 201 ? 1_555 102.7 ? 2 OP1 ? B C 8 ? B C 8 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 202 ? 1_555 98.2 ? 3 O ? O HOH . ? B HOH 201 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 202 ? 1_555 94.0 ? 4 OP1 ? B C 8 ? B C 8 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 203 ? 1_555 76.4 ? 5 O ? O HOH . ? B HOH 201 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 203 ? 1_555 178.9 ? 6 O ? O HOH . ? B HOH 202 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 203 ? 1_555 85.6 ? 7 OP1 ? B C 8 ? B C 8 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 204 ? 1_555 158.6 ? 8 O ? O HOH . ? B HOH 201 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 204 ? 1_555 96.6 ? 9 O ? O HOH . ? B HOH 202 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 204 ? 1_555 89.6 ? 10 O ? O HOH . ? B HOH 203 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 204 ? 1_555 84.4 ? 11 OP1 ? B C 8 ? B C 8 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 205 ? 1_555 81.2 ? 12 O ? O HOH . ? B HOH 201 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 205 ? 1_555 86.2 ? 13 O ? O HOH . ? B HOH 202 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 205 ? 1_555 179.5 ? 14 O ? O HOH . ? B HOH 203 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 205 ? 1_555 94.2 ? 15 O ? O HOH . ? B HOH 204 ? 1_555 MG ? I MG . ? B MG 103 ? 1_555 O ? O HOH . ? B HOH 205 ? 1_555 90.9 ? # 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 GAI 101 ? 4 'binding site for residue GAI A 101' AC2 Software A SPM 102 ? 8 'binding site for residue SPM A 102' AC3 Software B GAI 101 ? 4 'binding site for residue GAI B 101' AC4 Software B SPM 102 ? 5 'binding site for residue SPM B 102' AC5 Software B MG 103 ? 6 'binding site for residue MG B 103' AC6 Software C GAI 101 ? 4 'binding site for residue GAI C 101' AC7 Software C SPM 102 ? 7 'binding site for residue SPM C 102' AC8 Software D GAI 101 ? 4 'binding site for residue GAI D 101' AC9 Software D SPM 102 ? 5 'binding site for residue SPM D 102' AD1 Software B C 13 ? 8 'binding site for Di-nucleotide C B 13 and 5BU B 14' AD2 Software B 5BU 14 ? 9 'binding site for Di-nucleotide 5BU B 14 and G B 15' AD3 Software C C 13 ? 5 'binding site for Di-nucleotide C C 13 and 5BU C 14' AD4 Software C 5BU 14 ? 8 'binding site for Di-nucleotide 5BU C 14 and G C 15' AD5 Software D C 13 ? 5 'binding site for Di-nucleotide C D 13 and 5BU D 14' AD6 Software D 5BU 14 ? 6 'binding site for Di-nucleotide 5BU D 14 and G D 15' # 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 G A 6 ? G A 6 . ? 1_555 ? 2 AC1 4 A A 7 ? A A 7 . ? 1_555 ? 3 AC1 4 C A 8 ? C A 8 . ? 1_555 ? 4 AC1 4 G A 9 ? G A 9 . ? 1_555 ? 5 AC2 8 G A 5 ? G A 5 . ? 1_555 ? 6 AC2 8 G A 6 ? G A 6 . ? 1_555 ? 7 AC2 8 C A 8 ? C A 8 . ? 1_555 ? 8 AC2 8 G A 9 ? G A 9 . ? 1_555 ? 9 AC2 8 A A 10 ? A A 10 . ? 1_555 ? 10 AC2 8 HOH N . ? HOH A 201 . ? 1_555 ? 11 AC2 8 G C 15 ? G C 15 . ? 3_553 ? 12 AC2 8 C C 16 ? C C 16 . ? 3_553 ? 13 AC3 4 G B 6 ? G B 6 . ? 1_555 ? 14 AC3 4 A B 7 ? A B 7 . ? 1_555 ? 15 AC3 4 C B 8 ? C B 8 . ? 1_555 ? 16 AC3 4 G B 9 ? G B 9 . ? 1_555 ? 17 AC4 5 G B 3 ? G B 3 . ? 1_555 ? 18 AC4 5 G B 4 ? G B 4 . ? 1_555 ? 19 AC4 5 C B 12 ? C B 12 . ? 1_555 ? 20 AC4 5 C B 13 ? C B 13 . ? 1_555 ? 21 AC4 5 5BU B 14 ? 5BU B 14 . ? 1_555 ? 22 AC5 6 C B 8 ? C B 8 . ? 1_555 ? 23 AC5 6 HOH O . ? HOH B 201 . ? 1_555 ? 24 AC5 6 HOH O . ? HOH B 202 . ? 1_555 ? 25 AC5 6 HOH O . ? HOH B 203 . ? 1_555 ? 26 AC5 6 HOH O . ? HOH B 204 . ? 1_555 ? 27 AC5 6 HOH O . ? HOH B 205 . ? 1_555 ? 28 AC6 4 G C 6 ? G C 6 . ? 1_555 ? 29 AC6 4 A C 7 ? A C 7 . ? 1_555 ? 30 AC6 4 C C 8 ? C C 8 . ? 1_555 ? 31 AC6 4 G C 9 ? G C 9 . ? 1_555 ? 32 AC7 7 G A 15 ? G A 15 . ? 3_543 ? 33 AC7 7 C A 16 ? C A 16 . ? 3_543 ? 34 AC7 7 G C 5 ? G C 5 . ? 1_555 ? 35 AC7 7 G C 6 ? G C 6 . ? 1_555 ? 36 AC7 7 A C 7 ? A C 7 . ? 1_555 ? 37 AC7 7 C C 8 ? C C 8 . ? 1_555 ? 38 AC7 7 G C 9 ? G C 9 . ? 1_555 ? 39 AC8 4 G D 6 ? G D 6 . ? 1_555 ? 40 AC8 4 A D 7 ? A D 7 . ? 1_555 ? 41 AC8 4 C D 8 ? C D 8 . ? 1_555 ? 42 AC8 4 G D 9 ? G D 9 . ? 1_555 ? 43 AC9 5 G B 5 ? G B 5 . ? 4_464 ? 44 AC9 5 G D 5 ? G D 5 . ? 1_555 ? 45 AC9 5 G D 6 ? G D 6 . ? 1_555 ? 46 AC9 5 C D 8 ? C D 8 . ? 1_555 ? 47 AC9 5 G D 9 ? G D 9 . ? 1_555 ? 48 AD1 8 G B 3 ? G B 3 . ? 1_555 ? 49 AD1 8 G B 4 ? G B 4 . ? 1_555 ? 50 AD1 8 G B 5 ? G B 5 . ? 1_555 ? 51 AD1 8 C B 12 ? C B 12 . ? 1_555 ? 52 AD1 8 G B 15 ? G B 15 . ? 1_555 ? 53 AD1 8 SPM H . ? SPM B 102 . ? 1_555 ? 54 AD1 8 G D 9 ? G D 9 . ? 1_555 ? 55 AD1 8 A D 10 ? A D 10 . ? 1_555 ? 56 AD2 9 C B 2 ? C B 2 . ? 1_555 ? 57 AD2 9 G B 3 ? G B 3 . ? 1_555 ? 58 AD2 9 G B 4 ? G B 4 . ? 1_555 ? 59 AD2 9 C B 13 ? C B 13 . ? 1_555 ? 60 AD2 9 C B 16 ? C B 16 . ? 1_555 ? 61 AD2 9 SPM H . ? SPM B 102 . ? 1_555 ? 62 AD2 9 G D 3 ? G D 3 . ? 4_564 ? 63 AD2 9 G D 4 ? G D 4 . ? 4_564 ? 64 AD2 9 G D 9 ? G D 9 . ? 1_555 ? 65 AD3 5 G C 3 ? G C 3 . ? 1_555 ? 66 AD3 5 G C 4 ? G C 4 . ? 1_555 ? 67 AD3 5 G C 5 ? G C 5 . ? 1_555 ? 68 AD3 5 C C 12 ? C C 12 . ? 1_555 ? 69 AD3 5 G C 15 ? G C 15 . ? 1_555 ? 70 AD4 8 G A 5 ? G A 5 . ? 3_543 ? 71 AD4 8 G A 6 ? G A 6 . ? 3_543 ? 72 AD4 8 SPM F . ? SPM A 102 . ? 3_543 ? 73 AD4 8 C C 2 ? C C 2 . ? 1_555 ? 74 AD4 8 G C 3 ? G C 3 . ? 1_555 ? 75 AD4 8 G C 4 ? G C 4 . ? 1_555 ? 76 AD4 8 C C 13 ? C C 13 . ? 1_555 ? 77 AD4 8 C C 16 ? C C 16 . ? 1_555 ? 78 AD5 5 G D 3 ? G D 3 . ? 1_555 ? 79 AD5 5 G D 4 ? G D 4 . ? 1_555 ? 80 AD5 5 G D 5 ? G D 5 . ? 1_555 ? 81 AD5 5 C D 12 ? C D 12 . ? 1_555 ? 82 AD5 5 G D 15 ? G D 15 . ? 1_555 ? 83 AD6 6 C B 16 ? C B 16 . ? 4_464 ? 84 AD6 6 C D 2 ? C D 2 . ? 1_555 ? 85 AD6 6 G D 3 ? G D 3 . ? 1_555 ? 86 AD6 6 G D 4 ? G D 4 . ? 1_555 ? 87 AD6 6 C D 13 ? C D 13 . ? 1_555 ? 88 AD6 6 C D 16 ? C D 16 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" C G 9 ? ? P C A 10 ? ? 1.517 1.607 -0.090 0.012 Y 2 1 "O3'" C A 10 ? ? P C C 11 ? ? 1.511 1.607 -0.096 0.012 Y # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A A 7 ? ? P A A 7 ? ? OP1 A A 7 ? ? 98.91 105.70 -6.79 0.90 N 2 1 "O5'" B G 3 ? ? P B G 3 ? ? OP2 B G 3 ? ? 97.20 105.70 -8.50 0.90 N 3 1 "C4'" C G 9 ? ? "C3'" C G 9 ? ? "O3'" C G 9 ? ? 128.77 113.00 15.77 2.00 N # _phasing.method SAD # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 GAI C C N N 145 GAI N1 N N N 146 GAI N2 N N N 147 GAI N3 N N N 148 GAI HN1 H N N 149 GAI HN21 H N N 150 GAI HN22 H N N 151 GAI HN31 H N N 152 GAI HN32 H N N 153 HOH O O N N 154 HOH H1 H N N 155 HOH H2 H N N 156 MG MG MG N N 157 SPM N1 N N N 158 SPM C2 C N N 159 SPM C3 C N N 160 SPM C4 C N N 161 SPM N5 N N N 162 SPM C6 C N N 163 SPM C7 C N N 164 SPM C8 C N N 165 SPM C9 C N N 166 SPM N10 N N N 167 SPM C11 C N N 168 SPM C12 C N N 169 SPM C13 C N N 170 SPM N14 N N N 171 SPM HN11 H N N 172 SPM HN12 H N N 173 SPM H21 H N N 174 SPM H22 H N N 175 SPM H31 H N N 176 SPM H32 H N N 177 SPM H41 H N N 178 SPM H42 H N N 179 SPM HN5 H N N 180 SPM H61 H N N 181 SPM H62 H N N 182 SPM H71 H N N 183 SPM H72 H N N 184 SPM H81 H N N 185 SPM H82 H N N 186 SPM H91 H N N 187 SPM H92 H N N 188 SPM HN0 H N N 189 SPM H111 H N N 190 SPM H112 H N N 191 SPM H121 H N N 192 SPM H122 H N N 193 SPM H131 H N N 194 SPM H132 H N N 195 SPM HN41 H N N 196 SPM HN42 H N N 197 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 GAI C N1 doub N N 151 GAI C N2 sing N N 152 GAI C N3 sing N N 153 GAI N1 HN1 sing N N 154 GAI N2 HN21 sing N N 155 GAI N2 HN22 sing N N 156 GAI N3 HN31 sing N N 157 GAI N3 HN32 sing N N 158 HOH O H1 sing N N 159 HOH O H2 sing N N 160 SPM N1 C2 sing N N 161 SPM N1 HN11 sing N N 162 SPM N1 HN12 sing N N 163 SPM C2 C3 sing N N 164 SPM C2 H21 sing N N 165 SPM C2 H22 sing N N 166 SPM C3 C4 sing N N 167 SPM C3 H31 sing N N 168 SPM C3 H32 sing N N 169 SPM C4 N5 sing N N 170 SPM C4 H41 sing N N 171 SPM C4 H42 sing N N 172 SPM N5 C6 sing N N 173 SPM N5 HN5 sing N N 174 SPM C6 C7 sing N N 175 SPM C6 H61 sing N N 176 SPM C6 H62 sing N N 177 SPM C7 C8 sing N N 178 SPM C7 H71 sing N N 179 SPM C7 H72 sing N N 180 SPM C8 C9 sing N N 181 SPM C8 H81 sing N N 182 SPM C8 H82 sing N N 183 SPM C9 N10 sing N N 184 SPM C9 H91 sing N N 185 SPM C9 H92 sing N N 186 SPM N10 C11 sing N N 187 SPM N10 HN0 sing N N 188 SPM C11 C12 sing N N 189 SPM C11 H111 sing N N 190 SPM C11 H112 sing N N 191 SPM C12 C13 sing N N 192 SPM C12 H121 sing N N 193 SPM C12 H122 sing N N 194 SPM C13 N14 sing N N 195 SPM C13 H131 sing N N 196 SPM C13 H132 sing N N 197 SPM N14 HN41 sing N N 198 SPM N14 HN42 sing N N 199 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5VJB 'double helix' 5VJB 'a-form double helix' 5VJB 'hairpin loop' 5VJB 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 16 1_555 -0.071 -0.075 -0.061 -5.999 -3.055 0.370 1 A_G1:C16_A A 1 ? A 16 ? 19 1 1 A C 2 1_555 A G 15 1_555 0.152 -0.064 -0.056 1.966 -0.844 0.288 2 A_C2:G15_A A 2 ? A 15 ? 19 1 1 A G 3 1_555 A 5BU 14 1_555 -2.194 -0.714 -0.358 -7.017 -11.129 -5.191 3 A_G3:5BU14_A A 3 ? A 14 ? 28 1 1 A G 4 1_555 A C 13 1_555 -0.163 -0.086 -0.343 -7.642 -5.206 0.305 4 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A G 5 1_555 A C 12 1_555 -0.031 -0.186 -0.228 -4.142 -3.948 -2.671 5 A_G5:C12_A A 5 ? A 12 ? 19 1 1 A G 6 1_555 A C 11 1_555 0.024 -0.140 -0.241 -5.324 0.092 -1.391 6 A_G6:C11_A A 6 ? A 11 ? 19 1 1 B C 8 1_555 A G 9 1_555 0.239 -0.184 0.086 5.010 -11.604 1.167 7 B_C8:G9_A B 8 ? A 9 ? 19 1 1 B G 9 1_555 A C 8 1_555 -0.053 -0.131 0.059 -2.202 -10.520 -2.358 8 B_G9:C8_A B 9 ? A 8 ? 19 1 1 B C 11 1_555 B G 6 1_555 0.144 -0.071 -0.293 7.673 -4.260 -1.387 9 B_C11:G6_B B 11 ? B 6 ? 19 1 1 B C 12 1_555 B G 5 1_555 -0.032 -0.147 -0.216 4.832 -6.072 -2.011 10 B_C12:G5_B B 12 ? B 5 ? 19 1 1 B C 13 1_555 B G 4 1_555 0.049 -0.093 -0.210 7.261 -3.205 -2.313 11 B_C13:G4_B B 13 ? B 4 ? 19 1 1 B 5BU 14 1_555 B G 3 1_555 2.466 -0.632 -0.376 9.092 -16.765 -6.020 12 B_5BU14:G3_B B 14 ? B 3 ? 28 1 1 B G 15 1_555 B C 2 1_555 -0.396 -0.146 -0.195 -4.442 -6.494 1.170 13 B_G15:C2_B B 15 ? B 2 ? 19 1 1 B C 16 1_555 B G 1 1_555 0.252 -0.114 -0.012 6.991 -1.938 0.987 14 B_C16:G1_B B 16 ? B 1 ? 19 1 1 C G 1 1_555 C C 16 1_555 -0.284 -0.150 0.093 -0.925 0.409 0.892 15 C_G1:C16_C C 1 ? C 16 ? 19 1 1 C C 2 1_555 C G 15 1_555 0.218 -0.139 -0.157 6.994 -6.537 -0.721 16 C_C2:G15_C C 2 ? C 15 ? 19 1 1 C G 3 1_555 C 5BU 14 1_555 -2.179 -0.709 -0.051 -1.995 -13.587 -3.911 17 C_G3:5BU14_C C 3 ? C 14 ? 28 1 1 C G 4 1_555 C C 13 1_555 -0.316 -0.140 -0.301 -9.661 -5.220 1.245 18 C_G4:C13_C C 4 ? C 13 ? 19 1 1 C G 5 1_555 C C 12 1_555 0.068 -0.247 -0.149 -5.019 -1.537 0.036 19 C_G5:C12_C C 5 ? C 12 ? 19 1 1 C G 6 1_555 C C 11 1_555 0.136 -0.197 -0.055 -2.075 -0.464 -3.210 20 C_G6:C11_C C 6 ? C 11 ? 19 1 1 D C 8 1_555 C G 9 1_555 0.186 -0.186 0.020 4.479 -11.157 -1.570 21 D_C8:G9_C D 8 ? C 9 ? 19 1 1 D G 9 1_555 C C 8 1_555 0.000 -0.185 0.186 0.649 -6.138 -3.979 22 D_G9:C8_C D 9 ? C 8 ? 19 1 1 D C 11 1_555 D G 6 1_555 -0.087 -0.109 -0.168 3.030 -2.633 -2.720 23 D_C11:G6_D D 11 ? D 6 ? 19 1 1 D C 12 1_555 D G 5 1_555 0.080 0.012 -0.222 6.352 -4.478 -1.924 24 D_C12:G5_D D 12 ? D 5 ? 19 1 1 D C 13 1_555 D G 4 1_555 0.298 -0.070 -0.103 6.815 -4.720 0.180 25 D_C13:G4_D D 13 ? D 4 ? 19 1 1 D 5BU 14 1_555 D G 3 1_555 2.207 -0.602 -0.285 3.540 -12.868 -4.373 26 D_5BU14:G3_D D 14 ? D 3 ? 28 1 1 D G 15 1_555 D C 2 1_555 -0.154 -0.235 0.076 -4.290 -7.799 0.970 27 D_G15:C2_D D 15 ? D 2 ? 19 1 1 D C 16 1_555 D G 1 1_555 0.052 0.015 0.015 8.027 -5.113 3.100 28 D_C16:G1_D D 16 ? D 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 16 1_555 A C 2 1_555 A G 15 1_555 -0.337 -2.157 3.186 -0.223 -0.634 29.230 -4.139 0.621 3.233 -1.256 0.443 29.238 1 AA_G1C2:G15C16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A C 2 1_555 A G 15 1_555 A G 3 1_555 A 5BU 14 1_555 0.488 -2.312 3.471 2.477 9.612 18.307 -10.130 -0.390 2.056 27.722 -7.143 20.805 2 AA_C2G3:5BU14G15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A G 3 1_555 A 5BU 14 1_555 A G 4 1_555 A C 13 1_555 0.332 -1.607 3.363 -0.825 5.185 42.563 -2.715 -0.536 3.148 7.110 1.131 42.871 3 AA_G3G4:C135BU14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 1_555 A G 5 1_555 A C 12 1_555 -0.038 -1.887 3.302 0.197 3.036 29.220 -4.361 0.117 3.094 5.997 -0.389 29.374 4 AA_G4G5:C12C13_AA A 4 ? A 13 ? A 5 ? A 12 ? 1 A G 5 1_555 A C 12 1_555 A G 6 1_555 A C 11 1_555 0.244 -2.176 3.355 1.053 3.599 29.256 -5.031 -0.258 3.077 7.089 -2.073 29.490 5 AA_G5G6:C11C12_AA A 5 ? A 12 ? A 6 ? A 11 ? 1 A G 6 1_555 A C 11 1_555 B C 8 1_555 A G 9 1_555 -3.559 0.294 3.114 -5.663 -1.980 108.676 0.205 2.119 3.234 -1.218 3.484 108.789 6 AB_G6C8:G9C11_AA A 6 ? A 11 ? B 8 ? A 9 ? 1 B C 8 1_555 A G 9 1_555 B G 9 1_555 A C 8 1_555 -0.500 -1.387 3.501 0.298 6.473 36.948 -3.035 0.818 3.217 10.119 -0.466 37.492 7 BB_C8G9:C8G9_AA B 8 ? A 9 ? B 9 ? A 8 ? 1 B G 9 1_555 A C 8 1_555 B C 11 1_555 B G 6 1_555 3.690 0.077 3.161 3.337 -3.800 110.099 0.092 -2.210 3.233 -2.317 -2.035 110.177 8 BB_G9C11:G6C8_BA B 9 ? A 8 ? B 11 ? B 6 ? 1 B C 11 1_555 B G 6 1_555 B C 12 1_555 B G 5 1_555 -0.770 -2.078 3.378 -2.059 6.009 28.318 -5.443 1.094 2.931 12.091 4.142 29.008 9 BB_C11C12:G5G6_BB B 11 ? B 6 ? B 12 ? B 5 ? 1 B C 12 1_555 B G 5 1_555 B C 13 1_555 B G 4 1_555 -0.214 -1.944 3.291 -1.198 7.328 28.990 -5.189 0.182 2.734 14.343 2.345 29.906 10 BB_C12C13:G4G5_BB B 12 ? B 5 ? B 13 ? B 4 ? 1 B C 13 1_555 B G 4 1_555 B 5BU 14 1_555 B G 3 1_555 -0.140 -1.456 3.295 1.417 4.894 41.699 -2.530 0.340 3.106 6.845 -1.982 41.995 11 BB_C135BU14:G3G4_BB B 13 ? B 4 ? B 14 ? B 3 ? 1 B 5BU 14 1_555 B G 3 1_555 B G 15 1_555 B C 2 1_555 -0.094 -2.189 3.680 0.398 9.853 21.230 -8.692 0.365 2.432 25.074 -1.013 23.385 12 BB_5BU14G15:C2G3_BB B 14 ? B 3 ? B 15 ? B 2 ? 1 B G 15 1_555 B C 2 1_555 B C 16 1_555 B G 1 1_555 0.483 -1.826 3.078 -1.546 1.400 30.685 -3.697 -1.190 2.966 2.643 2.917 30.754 13 BB_G15C16:G1C2_BB B 15 ? B 2 ? B 16 ? B 1 ? 1 C G 1 1_555 C C 16 1_555 C C 2 1_555 C G 15 1_555 -0.537 -1.959 3.154 0.677 1.658 31.468 -3.898 1.109 3.038 3.054 -1.246 31.518 14 CC_G1C2:G15C16_CC C 1 ? C 16 ? C 2 ? C 15 ? 1 C C 2 1_555 C G 15 1_555 C G 3 1_555 C 5BU 14 1_555 0.194 -2.047 3.377 -2.436 10.584 21.832 -7.807 -1.140 2.134 25.976 5.978 24.355 15 CC_C2G3:5BU14G15_CC C 2 ? C 15 ? C 3 ? C 14 ? 1 C G 3 1_555 C 5BU 14 1_555 C G 4 1_555 C C 13 1_555 0.279 -1.655 3.584 0.982 3.806 40.715 -2.817 -0.283 3.428 5.455 -1.407 40.896 16 CC_G3G4:C135BU14_CC C 3 ? C 14 ? C 4 ? C 13 ? 1 C G 4 1_555 C C 13 1_555 C G 5 1_555 C C 12 1_555 0.105 -1.755 3.238 0.876 3.711 30.399 -4.024 -0.034 3.009 7.042 -1.663 30.632 17 CC_G4G5:C12C13_CC C 4 ? C 13 ? C 5 ? C 12 ? 1 C G 5 1_555 C C 12 1_555 C G 6 1_555 C C 11 1_555 0.022 -2.144 3.222 0.612 3.868 29.539 -4.933 0.077 2.924 7.544 -1.194 29.791 18 CC_G5G6:C11C12_CC C 5 ? C 12 ? C 6 ? C 11 ? 1 C G 6 1_555 C C 11 1_555 D C 8 1_555 C G 9 1_555 -3.513 0.158 3.097 -5.630 -2.675 106.201 0.133 2.122 3.221 -1.671 3.518 106.328 19 CD_G6C8:G9C11_CC C 6 ? C 11 ? D 8 ? C 9 ? 1 D C 8 1_555 C G 9 1_555 D G 9 1_555 C C 8 1_555 -0.220 -1.130 3.494 -0.731 4.501 36.936 -2.399 0.244 3.341 7.071 1.148 37.207 20 DD_C8G9:C8G9_CC D 8 ? C 9 ? D 9 ? C 8 ? 1 D G 9 1_555 C C 8 1_555 D C 11 1_555 D G 6 1_555 3.510 -0.129 3.238 7.867 -3.576 103.895 -0.030 -2.112 3.424 -2.268 -4.990 104.150 21 DD_G9C11:G6C8_DC D 9 ? C 8 ? D 11 ? D 6 ? 1 D C 11 1_555 D G 6 1_555 D C 12 1_555 D G 5 1_555 -0.149 -2.039 3.226 -1.491 3.279 30.426 -4.477 0.001 2.999 6.220 2.828 30.633 22 DD_C11C12:G5G6_DD D 11 ? D 6 ? D 12 ? D 5 ? 1 D C 12 1_555 D G 5 1_555 D C 13 1_555 D G 4 1_555 -0.075 -1.881 3.322 -1.750 4.269 31.250 -4.230 -0.179 3.044 7.870 3.227 31.581 23 DD_C12C13:G4G5_DD D 12 ? D 5 ? D 13 ? D 4 ? 1 D C 13 1_555 D G 4 1_555 D 5BU 14 1_555 D G 3 1_555 -0.365 -1.705 3.379 3.398 5.143 40.806 -2.973 0.883 3.112 7.326 -4.840 41.249 24 DD_C135BU14:G3G4_DD D 13 ? D 4 ? D 14 ? D 3 ? 1 D 5BU 14 1_555 D G 3 1_555 D G 15 1_555 D C 2 1_555 0.016 -1.812 3.307 -1.136 10.422 21.206 -7.502 -0.375 2.182 26.345 2.871 23.630 25 DD_5BU14G15:C2G3_DD D 14 ? D 3 ? D 15 ? D 2 ? 1 D G 15 1_555 D C 2 1_555 D C 16 1_555 D G 1 1_555 0.554 -1.925 3.082 1.377 -0.572 31.236 -3.468 -0.780 3.137 -1.061 -2.555 31.271 26 DD_G15C16:G1C2_DD D 15 ? D 2 ? D 16 ? D 1 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number GM022778 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 5VJB _atom_sites.fract_transf_matrix[1][1] 0.019907 _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] 0.016518 _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] 0.013905 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol BR C MG N O P # loop_