data_6HBT # _entry.id 6HBT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 6HBT pdb_00006hbt 10.2210/pdb6hbt/pdb WWPDB D_1200011437 ? ? # 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 2019-02-20 2 'Structure model' 1 1 2019-02-27 3 'Structure model' 1 2 2019-03-27 4 'Structure model' 2 0 2019-04-03 5 'Structure model' 2 1 2019-07-10 6 'Structure model' 2 2 2024-05-15 # _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 2 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Atomic model' 6 4 'Structure model' 'Data collection' 7 5 'Structure model' 'Data collection' 8 6 'Structure model' 'Data collection' 9 6 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' diffrn_source 2 2 'Structure model' pdbx_struct_assembly 3 2 'Structure model' pdbx_struct_assembly_gen 4 2 'Structure model' pdbx_struct_assembly_prop 5 2 'Structure model' pdbx_struct_oper_list 6 3 'Structure model' citation 7 3 'Structure model' citation_author 8 3 'Structure model' pdbx_database_proc 9 4 'Structure model' atom_site 10 5 'Structure model' diffrn_source 11 6 'Structure model' chem_comp_atom 12 6 'Structure model' chem_comp_bond 13 6 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 2 2 'Structure model' '_pdbx_struct_assembly.details' 3 2 'Structure model' '_pdbx_struct_assembly.method_details' 4 2 'Structure model' '_pdbx_struct_assembly.oligomeric_count' 5 2 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 6 3 'Structure model' '_citation.journal_abbrev' 7 3 'Structure model' '_citation.journal_volume' 8 3 'Structure model' '_citation.page_first' 9 3 'Structure model' '_citation.page_last' 10 3 'Structure model' '_citation.title' 11 3 'Structure model' '_citation_author.identifier_ORCID' 12 5 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 13 6 'Structure model' '_database_2.pdbx_DOI' 14 6 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6HBT _pdbx_database_status.recvd_initial_deposition_date 2018-08-13 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _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 'Huang, L.' 1 ? 'Lilley, D.M.J.' 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 25 _citation.language ? _citation.page_first 423 _citation.page_last 430 _citation.title 'Structure-guided design of a high-affinity ligand for a riboswitch.' _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1261/rna.069567.118 _citation.pdbx_database_id_PubMed 30609994 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, L.' 1 ? primary 'Wang, J.' 2 ? primary 'Wilson, T.J.' 3 ? primary 'Lilley, D.M.J.' 4 ? # 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*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3') ; 5880.434 1 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 3 non-polymer syn '1-(4-carbamimidamidobutyl)guanidine' 172.231 1 ? ? ? ? 4 water nat water 18.015 40 ? ? ? ? # _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 'GGUGGGGACGACCCCA(CBV)C' _entity_poly.pdbx_seq_one_letter_code_can GGUGGGGACGACCCCACC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SULFATE ION' SO4 3 '1-(4-carbamimidamidobutyl)guanidine' FXQ 4 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 G n 1 3 U n 1 4 G n 1 5 G n 1 6 G n 1 7 G n 1 8 A n 1 9 C n 1 10 G n 1 11 A n 1 12 C n 1 13 C n 1 14 C n 1 15 C n 1 16 A n 1 17 CBV n 1 18 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 18 _pdbx_entity_src_syn.organism_scientific 'Gloeobacter violaceus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 33072 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CBV 'RNA linking' n ;5-BROMOCYTIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C9 H13 Br N3 O8 P' 402.093 FXQ non-polymer . '1-(4-carbamimidamidobutyl)guanidine' ? 'C6 H16 N6' 172.231 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U 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 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 A 11 11 11 A A A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 C 15 15 15 C C A . n A 1 16 A 16 16 16 A A A . n A 1 17 CBV 17 17 17 CBV CBV A . n A 1 18 C 18 18 18 C C A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 SO4 1 101 1 SO4 SO4 A . C 2 SO4 1 102 2 SO4 SO4 A . D 3 FXQ 1 103 1 FXQ DRG A . E 4 HOH 1 201 20 HOH HOH A . E 4 HOH 2 202 33 HOH HOH A . E 4 HOH 3 203 8 HOH HOH A . E 4 HOH 4 204 24 HOH HOH A . E 4 HOH 5 205 10 HOH HOH A . E 4 HOH 6 206 17 HOH HOH A . E 4 HOH 7 207 7 HOH HOH A . E 4 HOH 8 208 32 HOH HOH A . E 4 HOH 9 209 3 HOH HOH A . E 4 HOH 10 210 40 HOH HOH A . E 4 HOH 11 211 5 HOH HOH A . E 4 HOH 12 212 35 HOH HOH A . E 4 HOH 13 213 6 HOH HOH A . E 4 HOH 14 214 25 HOH HOH A . E 4 HOH 15 215 16 HOH HOH A . E 4 HOH 16 216 26 HOH HOH A . E 4 HOH 17 217 2 HOH HOH A . E 4 HOH 18 218 14 HOH HOH A . E 4 HOH 19 219 4 HOH HOH A . E 4 HOH 20 220 19 HOH HOH A . E 4 HOH 21 221 38 HOH HOH A . E 4 HOH 22 222 1 HOH HOH A . E 4 HOH 23 223 13 HOH HOH A . E 4 HOH 24 224 34 HOH HOH A . E 4 HOH 25 225 22 HOH HOH A . E 4 HOH 26 226 15 HOH HOH A . E 4 HOH 27 227 29 HOH HOH A . E 4 HOH 28 228 21 HOH HOH A . E 4 HOH 29 229 11 HOH HOH A . E 4 HOH 30 230 28 HOH HOH A . E 4 HOH 31 231 37 HOH HOH A . E 4 HOH 32 232 9 HOH HOH A . E 4 HOH 33 233 31 HOH HOH A . E 4 HOH 34 234 27 HOH HOH A . E 4 HOH 35 235 39 HOH HOH A . E 4 HOH 36 236 12 HOH HOH A . E 4 HOH 37 237 36 HOH HOH A . E 4 HOH 38 238 18 HOH HOH A . E 4 HOH 39 239 23 HOH HOH A . E 4 HOH 40 240 30 HOH HOH A . # 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 ? ? ? '(1.14_3228: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? Aimless ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 6HBT _cell.details ? _cell.formula_units_Z ? _cell.length_a 55.460 _cell.length_a_esd ? _cell.length_b 55.460 _cell.length_b_esd ? _cell.length_c 135.040 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 18 _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 6HBT _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6HBT _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 3.40 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 63.81 _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 5.6 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;0.01 M Magnesium Acetate, 0.05 M MES pH 5.6, 2.5 M Ammonium Sulfate ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment ? # _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 2017-10-05 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9197 _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 'DIAMOND BEAMLINE I04' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9197 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I04 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6HBT _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.660 _reflns.d_resolution_low 27.730 _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 17902 _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 1.3 _reflns.percent_possible_obs 98.88 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 4.79 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 19.6 _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 0.028 _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.66 _reflns_shell.d_res_low 1.69 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 1.3 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 463 _reflns_shell.percent_possible_all 97.06 _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 1.316 _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 5.0 _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 0.647 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.571 _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 6HBT _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 1.660 _refine.ls_d_res_low 27.730 _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 17902 _refine.ls_number_reflns_R_free 821 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.61 _refine.ls_percent_reflns_R_free 4.59 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2066 _refine.ls_R_factor_R_free 0.2138 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2062 _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 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 SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 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 29.11 _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 0.24 _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 385 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 40 _refine_hist.number_atoms_total 447 _refine_hist.d_res_high 1.660 _refine_hist.d_res_low 27.730 # 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' ? 0.008 ? 449 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.195 ? 694 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 13.290 ? 211 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.055 ? 88 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.009 ? 18 ? 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' 1.6601 1.7640 . . 97 2865 97.00 . . . 0.3536 . 0.3082 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7640 1.9002 . . 188 2807 98.00 . . . 0.2903 . 0.2786 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9002 2.0914 . . 110 2859 98.00 . . . 0.2593 . 0.2429 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.0914 2.3939 . . 145 2896 99.00 . . . 0.2506 . 0.2210 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.3939 3.0154 . . 142 2846 98.00 . . . 0.1747 . 0.2308 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0154 27.7339 . . 139 2808 96.00 . . . 0.2019 . 0.1714 . . . . . . . . . . # _struct.entry_id 6HBT _struct.title 'The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with arcaine' _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 6HBT _struct_keywords.text 'guanidine II riboswitch, stem-loop, tetra loop, dimer, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? E N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6HBT _struct_ref.pdbx_db_accession 6HBT _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6HBT _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 18 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6HBT _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 18 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 18 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 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,C,D,E 1 2 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' 18_655 -x+4/3,-x+y+2/3,-z+2/3 -0.5000000000 -0.8660254038 0.0000000000 55.4600000000 -0.8660254038 0.5000000000 0.0000000000 32.0198459293 0.0000000000 0.0000000000 -1.0000000000 90.0266666667 # 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 A 16 "O3'" ? ? ? 1_555 A CBV 17 P ? ? A A 16 A CBV 17 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale one ? A CBV 17 "O3'" ? ? ? 1_555 A C 18 P ? ? A CBV 17 A C 18 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 1 A C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A CBV 17 N3 ? ? A G 2 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A CBV 17 O2 ? ? A G 2 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A CBV 17 N4 ? ? A G 2 A CBV 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 16 N1 ? ? A U 3 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 16 N6 ? ? A U 3 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 4 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 5 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 6 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 6 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 6 A C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 12 N3 ? ? A G 7 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 7 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 7 A C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SO4 101 ? 3 'binding site for residue SO4 A 101' AC2 Software A SO4 102 ? 4 'binding site for residue SO4 A 102' AC3 Software A FXQ 103 ? 8 'binding site for residue FXQ A 103' # 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 3 G A 2 ? G A 2 . ? 1_555 ? 2 AC1 3 U A 3 ? U A 3 . ? 1_555 ? 3 AC1 3 CBV A 17 ? CBV A 17 . ? 1_555 ? 4 AC2 4 HOH E . ? HOH A 203 . ? 1_555 ? 5 AC2 4 HOH E . ? HOH A 217 . ? 2_665 ? 6 AC2 4 HOH E . ? HOH A 217 . ? 3_565 ? 7 AC2 4 HOH E . ? HOH A 217 . ? 1_555 ? 8 AC3 8 G A 7 ? G A 7 . ? 1_555 ? 9 AC3 8 G A 7 ? G A 7 . ? 18_655 ? 10 AC3 8 A A 8 ? A A 8 . ? 1_555 ? 11 AC3 8 A A 8 ? A A 8 . ? 18_655 ? 12 AC3 8 C A 9 ? C A 9 . ? 18_655 ? 13 AC3 8 C A 9 ? C A 9 . ? 1_555 ? 14 AC3 8 G A 10 ? G A 10 . ? 18_655 ? 15 AC3 8 G A 10 ? G A 10 . ? 1_555 ? # 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 215 ? E HOH . 2 1 A HOH 217 ? E HOH . 3 1 A HOH 220 ? E HOH . 4 1 A HOH 222 ? 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CBV O3P O N N 73 CBV P P N N 74 CBV O1P O N N 75 CBV O2P O N N 76 CBV "O5'" O N N 77 CBV "C5'" C N N 78 CBV "C4'" C N R 79 CBV "O4'" O N N 80 CBV "C3'" C N S 81 CBV "O3'" O N N 82 CBV "C2'" C N R 83 CBV "O2'" O N N 84 CBV "C1'" C N R 85 CBV N1 N N N 86 CBV C2 C N N 87 CBV O2 O N N 88 CBV N3 N N N 89 CBV C4 C N N 90 CBV N4 N N N 91 CBV C5 C N N 92 CBV C6 C N N 93 CBV BR BR N N 94 CBV HO3P H N N 95 CBV HO1P H N N 96 CBV "H5'1" H N N 97 CBV "H5'2" H N N 98 CBV "H4'" H N N 99 CBV "H3'" H N N 100 CBV "HO3'" H N N 101 CBV "H2'" H N N 102 CBV "HO2'" H N N 103 CBV "H1'" H N N 104 CBV HN41 H N N 105 CBV HN42 H N N 106 CBV H6 H N N 107 FXQ CAD C N N 108 FXQ CAF C N N 109 FXQ CAG C N N 110 FXQ CAH C N N 111 FXQ CAI C N N 112 FXQ CAK C N N 113 FXQ NAA N N N 114 FXQ NAB N N N 115 FXQ NAC N N N 116 FXQ NAE N N N 117 FXQ NAJ N N N 118 FXQ NAL N N N 119 FXQ HAF H N N 120 FXQ HAG H N N 121 FXQ HAH H N N 122 FXQ HAI H N N 123 FXQ HAJ H N N 124 FXQ HAK H N N 125 FXQ HAM H N N 126 FXQ HAL H N N 127 FXQ HAR H N N 128 FXQ HAS H N N 129 FXQ HAO H N N 130 FXQ HAC H N N 131 FXQ HAE H N N 132 FXQ HAN H N N 133 FXQ HAP H N N 134 FXQ HAQ H N N 135 G OP3 O N N 136 G P P N N 137 G OP1 O N N 138 G OP2 O N N 139 G "O5'" O N N 140 G "C5'" C N N 141 G "C4'" C N R 142 G "O4'" O N N 143 G "C3'" C N S 144 G "O3'" O N N 145 G "C2'" C N R 146 G "O2'" O N N 147 G "C1'" C N R 148 G N9 N Y N 149 G C8 C Y N 150 G N7 N Y N 151 G C5 C Y N 152 G C6 C N N 153 G O6 O N N 154 G N1 N N N 155 G C2 C N N 156 G N2 N N N 157 G N3 N N N 158 G C4 C Y N 159 G HOP3 H N N 160 G HOP2 H N N 161 G "H5'" H N N 162 G "H5''" H N N 163 G "H4'" H N N 164 G "H3'" H N N 165 G "HO3'" H N N 166 G "H2'" H N N 167 G "HO2'" H N N 168 G "H1'" H N N 169 G H8 H N N 170 G H1 H N N 171 G H21 H N N 172 G H22 H N N 173 HOH O O N N 174 HOH H1 H N N 175 HOH H2 H N N 176 SO4 S S N N 177 SO4 O1 O N N 178 SO4 O2 O N N 179 SO4 O3 O N N 180 SO4 O4 O N N 181 U OP3 O N N 182 U P P N N 183 U OP1 O N N 184 U OP2 O N N 185 U "O5'" O N N 186 U "C5'" C N N 187 U "C4'" C N R 188 U "O4'" O N N 189 U "C3'" C N S 190 U "O3'" O N N 191 U "C2'" C N R 192 U "O2'" O N N 193 U "C1'" C N R 194 U N1 N N N 195 U C2 C N N 196 U O2 O N N 197 U N3 N N N 198 U C4 C N N 199 U O4 O N N 200 U C5 C N N 201 U C6 C N N 202 U HOP3 H N N 203 U HOP2 H N N 204 U "H5'" H N N 205 U "H5''" H N N 206 U "H4'" H N N 207 U "H3'" H N N 208 U "HO3'" H N N 209 U "H2'" H N N 210 U "HO2'" H N N 211 U "H1'" H N N 212 U H3 H N N 213 U H5 H N N 214 U H6 H N N 215 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 CBV O3P P sing N N 76 CBV O3P HO3P sing N N 77 CBV P O1P sing N N 78 CBV P O2P doub N N 79 CBV P "O5'" sing N N 80 CBV O1P HO1P sing N N 81 CBV "O5'" "C5'" sing N N 82 CBV "C5'" "C4'" sing N N 83 CBV "C5'" "H5'1" sing N N 84 CBV "C5'" "H5'2" sing N N 85 CBV "C4'" "O4'" sing N N 86 CBV "C4'" "C3'" sing N N 87 CBV "C4'" "H4'" sing N N 88 CBV "O4'" "C1'" sing N N 89 CBV "C3'" "O3'" sing N N 90 CBV "C3'" "C2'" sing N N 91 CBV "C3'" "H3'" sing N N 92 CBV "O3'" "HO3'" sing N N 93 CBV "C2'" "O2'" sing N N 94 CBV "C2'" "C1'" sing N N 95 CBV "C2'" "H2'" sing N N 96 CBV "O2'" "HO2'" sing N N 97 CBV "C1'" N1 sing N N 98 CBV "C1'" "H1'" sing N N 99 CBV N1 C2 sing N N 100 CBV N1 C6 sing N N 101 CBV C2 O2 doub N N 102 CBV C2 N3 sing N N 103 CBV N3 C4 doub N N 104 CBV C4 N4 sing N N 105 CBV C4 C5 sing N N 106 CBV N4 HN41 sing N N 107 CBV N4 HN42 sing N N 108 CBV C5 C6 doub N N 109 CBV C5 BR sing N N 110 CBV C6 H6 sing N N 111 FXQ NAB CAK doub N N 112 FXQ CAH CAI sing N N 113 FXQ CAH CAG sing N N 114 FXQ NAJ CAK sing N N 115 FXQ NAJ CAI sing N N 116 FXQ CAK NAL sing N N 117 FXQ NAA CAD doub N N 118 FXQ CAF CAG sing N N 119 FXQ CAF NAE sing N N 120 FXQ CAD NAE sing N N 121 FXQ CAD NAC sing N N 122 FXQ CAF HAF sing N N 123 FXQ CAF HAG sing N N 124 FXQ CAG HAH sing N N 125 FXQ CAG HAI sing N N 126 FXQ CAH HAJ sing N N 127 FXQ CAH HAK sing N N 128 FXQ CAI HAM sing N N 129 FXQ CAI HAL sing N N 130 FXQ NAA HAR sing N N 131 FXQ NAB HAS sing N N 132 FXQ NAC HAO sing N N 133 FXQ NAC HAC sing N N 134 FXQ NAE HAE sing N N 135 FXQ NAJ HAN sing N N 136 FXQ NAL HAP sing N N 137 FXQ NAL HAQ sing N N 138 G OP3 P sing N N 139 G OP3 HOP3 sing N N 140 G P OP1 doub N N 141 G P OP2 sing N N 142 G P "O5'" sing N N 143 G OP2 HOP2 sing N N 144 G "O5'" "C5'" sing N N 145 G "C5'" "C4'" sing N N 146 G "C5'" "H5'" sing N N 147 G "C5'" "H5''" sing N N 148 G "C4'" "O4'" sing N N 149 G "C4'" "C3'" sing N N 150 G "C4'" "H4'" sing N N 151 G "O4'" "C1'" sing N N 152 G "C3'" "O3'" sing N N 153 G "C3'" "C2'" sing N N 154 G "C3'" "H3'" sing N N 155 G "O3'" "HO3'" sing N N 156 G "C2'" "O2'" sing N N 157 G "C2'" "C1'" sing N N 158 G "C2'" "H2'" sing N N 159 G "O2'" "HO2'" sing N N 160 G "C1'" N9 sing N N 161 G "C1'" "H1'" sing N N 162 G N9 C8 sing Y N 163 G N9 C4 sing Y N 164 G C8 N7 doub Y N 165 G C8 H8 sing N N 166 G N7 C5 sing Y N 167 G C5 C6 sing N N 168 G C5 C4 doub Y N 169 G C6 O6 doub N N 170 G C6 N1 sing N N 171 G N1 C2 sing N N 172 G N1 H1 sing N N 173 G C2 N2 sing N N 174 G C2 N3 doub N N 175 G N2 H21 sing N N 176 G N2 H22 sing N N 177 G N3 C4 sing N N 178 HOH O H1 sing N N 179 HOH O H2 sing N N 180 SO4 S O1 doub N N 181 SO4 S O2 doub N N 182 SO4 S O3 sing N N 183 SO4 S O4 sing N N 184 U OP3 P sing N N 185 U OP3 HOP3 sing N N 186 U P OP1 doub N N 187 U P OP2 sing N N 188 U P "O5'" sing N N 189 U OP2 HOP2 sing N N 190 U "O5'" "C5'" sing N N 191 U "C5'" "C4'" sing N N 192 U "C5'" "H5'" sing N N 193 U "C5'" "H5''" sing N N 194 U "C4'" "O4'" sing N N 195 U "C4'" "C3'" sing N N 196 U "C4'" "H4'" sing N N 197 U "O4'" "C1'" sing N N 198 U "C3'" "O3'" sing N N 199 U "C3'" "C2'" sing N N 200 U "C3'" "H3'" sing N N 201 U "O3'" "HO3'" sing N N 202 U "C2'" "O2'" sing N N 203 U "C2'" "C1'" sing N N 204 U "C2'" "H2'" sing N N 205 U "O2'" "HO2'" sing N N 206 U "C1'" N1 sing N N 207 U "C1'" "H1'" sing N N 208 U N1 C2 sing N N 209 U N1 C6 sing N N 210 U C2 O2 doub N N 211 U C2 N3 sing N N 212 U N3 C4 sing N N 213 U N3 H3 sing N N 214 U C4 O4 doub N N 215 U C4 C5 sing N N 216 U C5 C6 doub N N 217 U C5 H5 sing N N 218 U C6 H6 sing N N 219 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 6HBT 'a-form double helix' 6HBT 'hairpin loop' 6HBT '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 18 1_555 -0.162 -0.119 -0.088 -4.823 -1.494 -1.707 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A G 2 1_555 A CBV 17 1_555 -0.279 -0.155 -0.031 -3.888 -11.563 0.070 2 A_G2:CBV17_A A 2 ? A 17 ? 19 1 1 A U 3 1_555 A A 16 1_555 -0.038 -0.074 0.031 0.120 -12.398 4.166 3 A_U3:A16_A A 3 ? A 16 ? 20 1 1 A G 4 1_555 A C 15 1_555 -0.301 -0.096 -0.295 -6.397 -8.090 0.767 4 A_G4:C15_A A 4 ? A 15 ? 19 1 1 A G 5 1_555 A C 14 1_555 -0.226 -0.191 -0.331 -10.611 -8.551 -3.030 5 A_G5:C14_A A 5 ? A 14 ? 19 1 1 A G 6 1_555 A C 13 1_555 -0.164 -0.084 -0.235 -10.079 -5.682 0.075 6 A_G6:C13_A A 6 ? A 13 ? 19 1 1 A G 7 1_555 A C 12 1_555 -0.231 -0.113 0.025 -2.250 3.993 -2.556 7 A_G7:C12_A A 7 ? A 12 ? 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 18 1_555 A G 2 1_555 A CBV 17 1_555 0.334 -1.988 3.330 1.665 2.083 28.744 -4.452 -0.300 3.195 4.185 -3.345 28.864 1 AA_G1G2:CBV17C18_AA A 1 ? A 18 ? A 2 ? A 17 ? 1 A G 2 1_555 A CBV 17 1_555 A U 3 1_555 A A 16 1_555 0.536 -1.785 3.212 0.145 2.511 32.646 -3.582 -0.927 3.072 4.458 -0.258 32.740 2 AA_G2U3:A16CBV17_AA A 2 ? A 17 ? A 3 ? A 16 ? 1 A U 3 1_555 A A 16 1_555 A G 4 1_555 A C 15 1_555 -0.473 -1.648 3.432 1.849 12.260 30.816 -4.854 1.125 2.576 21.987 -3.315 33.160 3 AA_U3G4:C15A16_AA A 3 ? A 16 ? A 4 ? A 15 ? 1 A G 4 1_555 A C 15 1_555 A G 5 1_555 A C 14 1_555 0.217 -2.111 3.437 0.970 8.278 28.293 -5.850 -0.226 2.729 16.488 -1.933 29.471 4 AA_G4G5:C14C15_AA A 4 ? A 15 ? A 5 ? A 14 ? 1 A G 5 1_555 A C 14 1_555 A G 6 1_555 A C 13 1_555 0.519 -1.918 3.336 1.257 5.141 30.944 -4.489 -0.730 3.004 9.547 -2.334 31.382 5 AA_G5G6:C13C14_AA A 5 ? A 14 ? A 6 ? A 13 ? 1 A G 6 1_555 A C 13 1_555 A G 7 1_555 A C 12 1_555 -0.341 -2.204 3.167 -0.810 1.624 28.019 -4.907 0.522 3.046 3.350 1.670 28.076 6 AA_G6G7:C12C13_AA A 6 ? A 13 ? A 7 ? A 12 ? # _pdbx_audit_support.funding_organization 'Cancer Research UK' _pdbx_audit_support.country 'United Kingdom' _pdbx_audit_support.grant_number A18604 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 6HBT _atom_sites.fract_transf_matrix[1][1] 0.018031 _atom_sites.fract_transf_matrix[1][2] 0.010410 _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] 0.020820 _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] 0.007405 _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 H N O P S # loop_