data_5NEQ # _entry.id 5NEQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 5NEQ pdb_00005neq 10.2210/pdb5neq/pdb WWPDB D_1200003985 ? ? # 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 2017-05-31 2 'Structure model' 1 1 2017-07-05 3 'Structure model' 1 2 2017-08-30 4 'Structure model' 1 3 2019-03-20 5 'Structure model' 1 4 2019-07-10 6 'Structure model' 1 5 2024-01-17 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Author supporting evidence' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Structure summary' 6 5 'Structure model' 'Data collection' 7 6 'Structure model' 'Data collection' 8 6 'Structure model' 'Database references' 9 6 'Structure model' 'Derived calculations' 10 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 3 'Structure model' pdbx_audit_support 3 4 'Structure model' diffrn_source 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_assembly_gen 6 4 'Structure model' pdbx_struct_assembly_prop 7 4 'Structure model' pdbx_struct_oper_list 8 4 'Structure model' struct_keywords 9 5 'Structure model' diffrn_source 10 6 'Structure model' chem_comp_atom 11 6 'Structure model' chem_comp_bond 12 6 'Structure model' database_2 13 6 'Structure model' pdbx_initial_refinement_model 14 6 'Structure model' struct_conn 15 6 'Structure model' struct_conn_type # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_volume' 3 2 'Structure model' '_citation.page_first' 4 2 'Structure model' '_citation.page_last' 5 3 'Structure model' '_pdbx_audit_support.funding_organization' 6 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 7 4 'Structure model' '_pdbx_struct_assembly.details' 8 4 'Structure model' '_pdbx_struct_assembly.method_details' 9 4 'Structure model' '_pdbx_struct_assembly.oligomeric_count' 10 4 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 11 4 'Structure model' '_struct_keywords.text' 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' 15 6 'Structure model' '_struct_conn.conn_type_id' 16 6 'Structure model' '_struct_conn.id' 17 6 'Structure model' '_struct_conn.pdbx_dist_value' 18 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 19 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 26 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 27 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 28 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 29 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 30 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 31 6 'Structure model' '_struct_conn.ptnr2_symmetry' 32 6 'Structure model' '_struct_conn_type.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 5NEQ _pdbx_database_status.recvd_initial_deposition_date 2017-03-11 _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 ? 'Wang, J.' 2 ? 'Lilley, D.M.J.' 3 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Cell Chem Biol' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2451-9456 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 24 _citation.language ? _citation.page_first 695 _citation.page_last 702.e2 _citation.title 'The Structure of the Guanidine-II Riboswitch.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.chembiol.2017.05.014 _citation.pdbx_database_id_PubMed 28529131 _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 'Lilley, D.M.J.' 3 ? # 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 AMINOGUANIDINE 74.085 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 7 ? ? ? ? 5 water nat water 18.015 35 ? ? ? ? # _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 AMINOGUANIDINE AGU 3 'SULFATE ION' SO4 4 'SODIUM ION' NA 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 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 AGU non-polymer . AMINOGUANIDINE ? 'C H6 N4' 74.085 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 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 AGU 1 101 1 AGU AGU A . C 3 SO4 1 102 1 SO4 SO4 A . D 3 SO4 1 103 2 SO4 SO4 A . E 4 NA 1 104 1 NA NA A . F 4 NA 1 105 2 NA NA A . G 4 NA 1 106 3 NA NA A . H 4 NA 1 107 4 NA NA A . I 4 NA 1 108 5 NA NA A . J 4 NA 1 109 6 NA NA A . K 4 NA 1 110 7 NA NA A . L 5 HOH 1 201 27 HOH HOH A . L 5 HOH 2 202 23 HOH HOH A . L 5 HOH 3 203 19 HOH HOH A . L 5 HOH 4 204 6 HOH HOH A . L 5 HOH 5 205 2 HOH HOH A . L 5 HOH 6 206 7 HOH HOH A . L 5 HOH 7 207 21 HOH HOH A . L 5 HOH 8 208 11 HOH HOH A . L 5 HOH 9 209 31 HOH HOH A . L 5 HOH 10 210 33 HOH HOH A . L 5 HOH 11 211 16 HOH HOH A . L 5 HOH 12 212 25 HOH HOH A . L 5 HOH 13 213 5 HOH HOH A . L 5 HOH 14 214 14 HOH HOH A . L 5 HOH 15 215 36 HOH HOH A . L 5 HOH 16 216 32 HOH HOH A . L 5 HOH 17 217 12 HOH HOH A . L 5 HOH 18 218 1 HOH HOH A . L 5 HOH 19 219 18 HOH HOH A . L 5 HOH 20 220 24 HOH HOH A . L 5 HOH 21 221 4 HOH HOH A . L 5 HOH 22 222 3 HOH HOH A . L 5 HOH 23 223 26 HOH HOH A . L 5 HOH 24 224 37 HOH HOH A . L 5 HOH 25 225 10 HOH HOH A . L 5 HOH 26 226 22 HOH HOH A . L 5 HOH 27 227 8 HOH HOH A . L 5 HOH 28 228 30 HOH HOH A . L 5 HOH 29 229 20 HOH HOH A . L 5 HOH 30 230 35 HOH HOH A . L 5 HOH 31 231 15 HOH HOH A . L 5 HOH 32 232 17 HOH HOH A . L 5 HOH 33 233 34 HOH HOH A . L 5 HOH 34 234 13 HOH HOH A . L 5 HOH 35 235 28 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 ? ? ? '(dev_2219: ???)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 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 5NEQ _cell.details ? _cell.formula_units_Z ? _cell.length_a 55.463 _cell.length_a_esd ? _cell.length_b 55.463 _cell.length_b_esd ? _cell.length_c 130.276 _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 5NEQ _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 5NEQ _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 3.28 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 62.49 _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 ? _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_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS3 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2017-03-04 # _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 0.9201 _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 I24' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9201 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I24 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate 35.4 _reflns.entry_id 5NEQ _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.69 _reflns.d_resolution_low 38.66 _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 16376 _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 99.8 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 14.13 _reflns.pdbx_Rmerge_I_obs 0.0716 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 13.7 _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 0.02 _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 1.69 _reflns_shell.d_res_low 1.72 _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 436 _reflns_shell.percent_possible_all 99.5 _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 1.5 _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 13.4 _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 0.713 _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.866 _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 5NEQ _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 1.690 _refine.ls_d_res_low 38.658 _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 16376 _refine.ls_number_reflns_R_free 891 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.77 _refine.ls_percent_reflns_R_free 5.44 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2178 _refine.ls_R_factor_R_free 0.2524 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2157 _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 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 5NEO _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 33.89 _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 0.27 _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 386 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 35 _refine_hist.number_atoms_total 443 _refine_hist.d_res_high 1.690 _refine_hist.d_res_low 38.658 # 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' ? 0.011 ? 443 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.777 ? 689 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 9.694 ? 204 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.067 ? 88 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.015 ? 19 ? 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' 1.6904 1.7963 . . 119 2509 94.00 . . . 0.3928 . 0.3914 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.7963 1.9350 . . 136 2554 97.00 . . . 0.3903 . 0.3656 . . . . . . . . . . 'X-RAY DIFFRACTION' 1.9350 2.1297 . . 172 2587 99.00 . . . 0.4049 . 0.2953 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.1297 2.4379 . . 168 2595 99.00 . . . 0.2668 . 0.2333 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.4379 3.0712 . . 147 2629 99.00 . . . 0.2583 . 0.2284 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0712 38.6685 . . 149 2611 99.00 . . . 0.1991 . 0.1638 . . . . . . . . . . # _struct.entry_id 5NEQ _struct.title 'The structure of the G. violaceus guanidine II riboswitch P1 stem-loop with aminoguanidine' _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 5NEQ _struct_keywords.text 'guanidine II riboswitch, stem-loop, tetra loop, dimer, aminoguanidine, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 4 ? I N N 4 ? J N N 4 ? K N N 4 ? L N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5NEQ _struct_ref.pdbx_db_accession 5NEQ _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 5NEQ _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 5NEQ _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,F,G,H,I,J,K,L 1 2 A,B,C,D,E,F,G,H,I,J,K,L # _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' 10_455 y-1/3,x+1/3,-z+1/3 -0.5000000000 0.8660254038 0.0000000000 -27.7315000000 0.8660254038 0.5000000000 0.0000000000 16.0107889900 0.0000000000 0.0000000000 -1.0000000000 43.4253333333 # 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 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale one ? A CBV 17 "O3'" ? ? ? 1_555 A C 18 P ? ? A CBV 17 A C 18 1_555 ? ? ? ? ? ? ? 1.596 ? ? metalc1 metalc ? ? A G 7 O6 ? ? ? 1_555 K NA . NA ? ? A G 7 A NA 110 1_555 ? ? ? ? ? ? ? 2.959 ? ? metalc2 metalc ? ? A A 8 OP1 ? ? ? 1_555 I NA . NA ? ? A A 8 A NA 108 1_555 ? ? ? ? ? ? ? 2.398 ? ? metalc3 metalc ? ? A G 10 OP2 ? ? ? 1_555 K NA . NA ? ? A G 10 A NA 110 1_555 ? ? ? ? ? ? ? 2.816 ? ? metalc4 metalc ? ? A C 12 OP2 ? ? ? 1_555 H NA . NA ? ? A C 12 A NA 107 1_555 ? ? ? ? ? ? ? 2.898 ? ? metalc5 metalc ? ? A C 13 OP2 ? ? ? 1_555 H NA . NA ? ? A C 13 A NA 107 1_555 ? ? ? ? ? ? ? 2.724 ? ? metalc6 metalc ? ? E NA . NA ? ? ? 1_555 L HOH . O ? ? A NA 104 A HOH 201 1_555 ? ? ? ? ? ? ? 2.828 ? ? metalc7 metalc ? ? E NA . NA ? ? ? 1_555 L HOH . O ? ? A NA 104 A HOH 232 1_555 ? ? ? ? ? ? ? 2.407 ? ? metalc8 metalc ? ? I NA . NA ? ? ? 1_555 L HOH . O ? ? A NA 108 A HOH 229 10_455 ? ? ? ? ? ? ? 2.426 ? ? metalc9 metalc ? ? K NA . NA ? ? ? 1_555 L HOH . O ? ? A NA 110 A HOH 233 1_555 ? ? ? ? ? ? ? 2.271 ? ? 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 ? ? 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 O6 ? A G 7 ? A G 7 ? 1_555 NA ? K NA . ? A NA 110 ? 1_555 OP2 ? A G 10 ? A G 10 ? 1_555 95.7 ? 2 O6 ? A G 7 ? A G 7 ? 1_555 NA ? K NA . ? A NA 110 ? 1_555 O ? L HOH . ? A HOH 233 ? 1_555 84.8 ? 3 OP2 ? A G 10 ? A G 10 ? 1_555 NA ? K NA . ? A NA 110 ? 1_555 O ? L HOH . ? A HOH 233 ? 1_555 102.6 ? 4 OP1 ? A A 8 ? A A 8 ? 1_555 NA ? I NA . ? A NA 108 ? 1_555 O ? L HOH . ? A HOH 229 ? 10_455 155.5 ? 5 OP2 ? A C 12 ? A C 12 ? 1_555 NA ? H NA . ? A NA 107 ? 1_555 OP2 ? A C 13 ? A C 13 ? 1_555 103.6 ? 6 O ? L HOH . ? A HOH 201 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 O ? L HOH . ? A HOH 232 ? 1_555 169.3 ? # 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 AGU 101 ? 6 'binding site for residue AGU A 101' AC2 Software A SO4 102 ? 4 'binding site for residue SO4 A 102' AC3 Software A SO4 103 ? 3 'binding site for residue SO4 A 103' AC4 Software A NA 104 ? 3 'binding site for residue NA A 104' AC5 Software A NA 105 ? 1 'binding site for residue NA A 105' AC6 Software A NA 107 ? 2 'binding site for residue NA A 107' AC7 Software A NA 108 ? 4 'binding site for residue NA A 108' AC8 Software A NA 109 ? 1 'binding site for residue NA A 109' AC9 Software A NA 110 ? 4 'binding site for residue NA A 110' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 G A 7 ? G A 7 . ? 1_555 ? 2 AC1 6 A A 8 ? A A 8 . ? 1_555 ? 3 AC1 6 C A 9 ? C A 9 . ? 1_555 ? 4 AC1 6 G A 10 ? G A 10 . ? 1_555 ? 5 AC1 6 NA I . ? NA A 108 . ? 1_555 ? 6 AC1 6 NA K . ? NA A 110 . ? 1_555 ? 7 AC2 4 G A 2 ? G A 2 . ? 1_555 ? 8 AC2 4 U A 3 ? U A 3 . ? 1_555 ? 9 AC2 4 C A 15 ? C A 15 . ? 2_565 ? 10 AC2 4 HOH L . ? HOH A 203 . ? 2_565 ? 11 AC3 3 CBV A 17 ? CBV A 17 . ? 1_555 ? 12 AC3 3 HOH L . ? HOH A 201 . ? 1_555 ? 13 AC3 3 HOH L . ? HOH A 219 . ? 1_555 ? 14 AC4 3 C A 15 ? C A 15 . ? 1_555 ? 15 AC4 3 HOH L . ? HOH A 201 . ? 1_555 ? 16 AC4 3 HOH L . ? HOH A 232 . ? 1_555 ? 17 AC5 1 G A 2 ? G A 2 . ? 1_555 ? 18 AC6 2 C A 12 ? C A 12 . ? 1_555 ? 19 AC6 2 C A 13 ? C A 13 . ? 1_555 ? 20 AC7 4 A A 8 ? A A 8 . ? 1_555 ? 21 AC7 4 C A 9 ? C A 9 . ? 1_555 ? 22 AC7 4 AGU B . ? AGU A 101 . ? 1_555 ? 23 AC7 4 HOH L . ? HOH A 229 . ? 10_455 ? 24 AC8 1 G A 1 ? G A 1 . ? 1_555 ? 25 AC9 4 G A 7 ? G A 7 . ? 1_555 ? 26 AC9 4 G A 10 ? G A 10 . ? 1_555 ? 27 AC9 4 AGU B . ? AGU A 101 . ? 1_555 ? 28 AC9 4 HOH L . ? HOH A 233 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "O3'" A A 16 ? ? O3P A CBV 17 ? ? 0.36 2 1 "HO3'" A CBV 17 ? ? P A C 18 ? ? 0.79 3 1 "C3'" A A 16 ? ? O3P A CBV 17 ? ? 1.77 # 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 G 5 ? ? P A G 5 ? ? OP2 A G 5 ? ? 98.89 105.70 -6.81 0.90 N 2 1 C8 A G 6 ? ? N9 A G 6 ? ? C4 A G 6 ? ? 103.98 106.40 -2.43 0.40 N # 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 217 ? L HOH . 2 1 A HOH 218 ? L HOH . 3 1 A HOH 222 ? L HOH . 4 1 A HOH 227 ? L HOH . 5 1 A HOH 231 ? L HOH . 6 1 A HOH 235 ? L HOH . # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -18.2109 21.2140 14.9090 0.3709 0.3157 0.2839 0.0083 0.0268 -0.0204 0.7494 2.8701 2.6624 0.5164 1.0772 -3.1853 -0.0044 0.0071 -0.0214 0.3585 0.0904 -0.0355 -0.1918 0.1493 -0.0510 'X-RAY DIFFRACTION' 2 ? refined -16.1149 18.6150 8.5246 0.2590 0.2955 0.2770 -0.0373 -0.0012 0.0254 6.7069 3.1781 5.9986 -2.2368 3.7262 -3.9459 -0.1632 0.1191 0.2648 0.2501 -0.2275 -0.2569 -0.5007 0.4853 0.3861 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 1 through 10 ) ; 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? ;chain 'A' and (resid 11 through 18 ) ; # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 235 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.21 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # 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 AGU C C N N 38 AGU N1 N N N 39 AGU N2 N N N 40 AGU N3 N N N 41 AGU N4 N N N 42 AGU HN1 H N N 43 AGU HN21 H N N 44 AGU HN22 H N N 45 AGU HN3 H N N 46 AGU HN41 H N N 47 AGU HN42 H N N 48 C OP3 O N N 49 C P P N N 50 C OP1 O N N 51 C OP2 O N N 52 C "O5'" O N N 53 C "C5'" C N N 54 C "C4'" C N R 55 C "O4'" O N N 56 C "C3'" C N S 57 C "O3'" O N N 58 C "C2'" C N R 59 C "O2'" O N N 60 C "C1'" C N R 61 C N1 N N N 62 C C2 C N N 63 C O2 O N N 64 C N3 N N N 65 C C4 C N N 66 C N4 N N N 67 C C5 C N N 68 C C6 C N N 69 C HOP3 H N N 70 C HOP2 H N N 71 C "H5'" H N N 72 C "H5''" H N N 73 C "H4'" H N N 74 C "H3'" H N N 75 C "HO3'" H N N 76 C "H2'" H N N 77 C "HO2'" H N N 78 C "H1'" H N N 79 C H41 H N N 80 C H42 H N N 81 C H5 H N N 82 C H6 H N N 83 CBV O3P O N N 84 CBV P P N N 85 CBV O1P O N N 86 CBV O2P O N N 87 CBV "O5'" O N N 88 CBV "C5'" C N N 89 CBV "C4'" C N R 90 CBV "O4'" O N N 91 CBV "C3'" C N S 92 CBV "O3'" O N N 93 CBV "C2'" C N R 94 CBV "O2'" O N N 95 CBV "C1'" C N R 96 CBV N1 N N N 97 CBV C2 C N N 98 CBV O2 O N N 99 CBV N3 N N N 100 CBV C4 C N N 101 CBV N4 N N N 102 CBV C5 C N N 103 CBV C6 C N N 104 CBV BR BR N N 105 CBV HO3P H N N 106 CBV HO1P H N N 107 CBV "H5'1" H N N 108 CBV "H5'2" H N N 109 CBV "H4'" H N N 110 CBV "H3'" H N N 111 CBV "HO3'" H N N 112 CBV "H2'" H N N 113 CBV "HO2'" H N N 114 CBV "H1'" H N N 115 CBV HN41 H N N 116 CBV HN42 H N N 117 CBV H6 H N N 118 G OP3 O N N 119 G P P N N 120 G OP1 O N N 121 G OP2 O N N 122 G "O5'" O N N 123 G "C5'" C N N 124 G "C4'" C N R 125 G "O4'" O N N 126 G "C3'" C N S 127 G "O3'" O N N 128 G "C2'" C N R 129 G "O2'" O N N 130 G "C1'" C N R 131 G N9 N Y N 132 G C8 C Y N 133 G N7 N Y N 134 G C5 C Y N 135 G C6 C N N 136 G O6 O N N 137 G N1 N N N 138 G C2 C N N 139 G N2 N N N 140 G N3 N N N 141 G C4 C Y N 142 G HOP3 H N N 143 G HOP2 H N N 144 G "H5'" H N N 145 G "H5''" H N N 146 G "H4'" H N N 147 G "H3'" H N N 148 G "HO3'" H N N 149 G "H2'" H N N 150 G "HO2'" H N N 151 G "H1'" H N N 152 G H8 H N N 153 G H1 H N N 154 G H21 H N N 155 G H22 H N N 156 HOH O O N N 157 HOH H1 H N N 158 HOH H2 H N N 159 NA NA NA N N 160 SO4 S S N N 161 SO4 O1 O N N 162 SO4 O2 O N N 163 SO4 O3 O N N 164 SO4 O4 O N N 165 U OP3 O N N 166 U P P N N 167 U OP1 O N N 168 U OP2 O N N 169 U "O5'" O N N 170 U "C5'" C N N 171 U "C4'" C N R 172 U "O4'" O N N 173 U "C3'" C N S 174 U "O3'" O N N 175 U "C2'" C N R 176 U "O2'" O N N 177 U "C1'" C N R 178 U N1 N N N 179 U C2 C N N 180 U O2 O N N 181 U N3 N N N 182 U C4 C N N 183 U O4 O N N 184 U C5 C N N 185 U C6 C N N 186 U HOP3 H N N 187 U HOP2 H N N 188 U "H5'" H N N 189 U "H5''" H N N 190 U "H4'" H N N 191 U "H3'" H N N 192 U "HO3'" H N N 193 U "H2'" H N N 194 U "HO2'" H N N 195 U "H1'" H N N 196 U H3 H N N 197 U H5 H N N 198 U H6 H N N 199 # 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 AGU C N1 doub N N 40 AGU C N2 sing N N 41 AGU C N3 sing N N 42 AGU N1 HN1 sing N N 43 AGU N2 HN21 sing N N 44 AGU N2 HN22 sing N N 45 AGU N3 N4 sing N N 46 AGU N3 HN3 sing N N 47 AGU N4 HN41 sing N N 48 AGU N4 HN42 sing N N 49 C OP3 P sing N N 50 C OP3 HOP3 sing N N 51 C P OP1 doub N N 52 C P OP2 sing N N 53 C P "O5'" sing N N 54 C OP2 HOP2 sing N N 55 C "O5'" "C5'" sing N N 56 C "C5'" "C4'" sing N N 57 C "C5'" "H5'" sing N N 58 C "C5'" "H5''" sing N N 59 C "C4'" "O4'" sing N N 60 C "C4'" "C3'" sing N N 61 C "C4'" "H4'" sing N N 62 C "O4'" "C1'" sing N N 63 C "C3'" "O3'" sing N N 64 C "C3'" "C2'" sing N N 65 C "C3'" "H3'" sing N N 66 C "O3'" "HO3'" sing N N 67 C "C2'" "O2'" sing N N 68 C "C2'" "C1'" sing N N 69 C "C2'" "H2'" sing N N 70 C "O2'" "HO2'" sing N N 71 C "C1'" N1 sing N N 72 C "C1'" "H1'" sing N N 73 C N1 C2 sing N N 74 C N1 C6 sing N N 75 C C2 O2 doub N N 76 C C2 N3 sing N N 77 C N3 C4 doub N N 78 C C4 N4 sing N N 79 C C4 C5 sing N N 80 C N4 H41 sing N N 81 C N4 H42 sing N N 82 C C5 C6 doub N N 83 C C5 H5 sing N N 84 C C6 H6 sing N N 85 CBV O3P P sing N N 86 CBV O3P HO3P sing N N 87 CBV P O1P sing N N 88 CBV P O2P doub N N 89 CBV P "O5'" sing N N 90 CBV O1P HO1P sing N N 91 CBV "O5'" "C5'" sing N N 92 CBV "C5'" "C4'" sing N N 93 CBV "C5'" "H5'1" sing N N 94 CBV "C5'" "H5'2" sing N N 95 CBV "C4'" "O4'" sing N N 96 CBV "C4'" "C3'" sing N N 97 CBV "C4'" "H4'" sing N N 98 CBV "O4'" "C1'" sing N N 99 CBV "C3'" "O3'" sing N N 100 CBV "C3'" "C2'" sing N N 101 CBV "C3'" "H3'" sing N N 102 CBV "O3'" "HO3'" sing N N 103 CBV "C2'" "O2'" sing N N 104 CBV "C2'" "C1'" sing N N 105 CBV "C2'" "H2'" sing N N 106 CBV "O2'" "HO2'" sing N N 107 CBV "C1'" N1 sing N N 108 CBV "C1'" "H1'" sing N N 109 CBV N1 C2 sing N N 110 CBV N1 C6 sing N N 111 CBV C2 O2 doub N N 112 CBV C2 N3 sing N N 113 CBV N3 C4 doub N N 114 CBV C4 N4 sing N N 115 CBV C4 C5 sing N N 116 CBV N4 HN41 sing N N 117 CBV N4 HN42 sing N N 118 CBV C5 C6 doub N N 119 CBV C5 BR sing N N 120 CBV C6 H6 sing N N 121 G OP3 P sing N N 122 G OP3 HOP3 sing N N 123 G P OP1 doub N N 124 G P OP2 sing N N 125 G P "O5'" sing N N 126 G OP2 HOP2 sing N N 127 G "O5'" "C5'" sing N N 128 G "C5'" "C4'" sing N N 129 G "C5'" "H5'" sing N N 130 G "C5'" "H5''" sing N N 131 G "C4'" "O4'" sing N N 132 G "C4'" "C3'" sing N N 133 G "C4'" "H4'" sing N N 134 G "O4'" "C1'" sing N N 135 G "C3'" "O3'" sing N N 136 G "C3'" "C2'" sing N N 137 G "C3'" "H3'" sing N N 138 G "O3'" "HO3'" sing N N 139 G "C2'" "O2'" sing N N 140 G "C2'" "C1'" sing N N 141 G "C2'" "H2'" sing N N 142 G "O2'" "HO2'" sing N N 143 G "C1'" N9 sing N N 144 G "C1'" "H1'" sing N N 145 G N9 C8 sing Y N 146 G N9 C4 sing Y N 147 G C8 N7 doub Y N 148 G C8 H8 sing N N 149 G N7 C5 sing Y N 150 G C5 C6 sing N N 151 G C5 C4 doub Y N 152 G C6 O6 doub N N 153 G C6 N1 sing N N 154 G N1 C2 sing N N 155 G N1 H1 sing N N 156 G C2 N2 sing N N 157 G C2 N3 doub N N 158 G N2 H21 sing N N 159 G N2 H22 sing N N 160 G N3 C4 sing N N 161 HOH O H1 sing N N 162 HOH O H2 sing N N 163 SO4 S O1 doub N N 164 SO4 S O2 doub N N 165 SO4 S O3 sing N N 166 SO4 S O4 sing N N 167 U OP3 P sing N N 168 U OP3 HOP3 sing N N 169 U P OP1 doub N N 170 U P OP2 sing N N 171 U P "O5'" sing N N 172 U OP2 HOP2 sing N N 173 U "O5'" "C5'" sing N N 174 U "C5'" "C4'" sing N N 175 U "C5'" "H5'" sing N N 176 U "C5'" "H5''" sing N N 177 U "C4'" "O4'" sing N N 178 U "C4'" "C3'" sing N N 179 U "C4'" "H4'" sing N N 180 U "O4'" "C1'" sing N N 181 U "C3'" "O3'" sing N N 182 U "C3'" "C2'" sing N N 183 U "C3'" "H3'" sing N N 184 U "O3'" "HO3'" sing N N 185 U "C2'" "O2'" sing N N 186 U "C2'" "C1'" sing N N 187 U "C2'" "H2'" sing N N 188 U "O2'" "HO2'" sing N N 189 U "C1'" N1 sing N N 190 U "C1'" "H1'" sing N N 191 U N1 C2 sing N N 192 U N1 C6 sing N N 193 U C2 O2 doub N N 194 U C2 N3 sing N N 195 U N3 C4 sing N N 196 U N3 H3 sing N N 197 U C4 O4 doub N N 198 U C4 C5 sing N N 199 U C5 C6 doub N N 200 U C5 H5 sing N N 201 U C6 H6 sing N N 202 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5NEQ 'a-form double helix' 5NEQ 'hairpin loop' 5NEQ '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 -0.113 -0.124 -0.215 -7.003 -1.663 -0.883 1 A_G1:C18_A A 1 ? A 18 ? 19 1 1 A G 2 1_555 A CBV 17 1_555 -0.509 -0.148 0.003 -3.967 -13.168 1.906 2 A_G2:CBV17_A A 2 ? A 17 ? 19 1 1 A U 3 1_555 A A 16 1_555 0.023 -0.116 0.078 -0.694 -12.534 4.014 3 A_U3:A16_A A 3 ? A 16 ? 20 1 1 A G 4 1_555 A C 15 1_555 -0.257 -0.081 -0.381 -7.284 -9.983 0.042 4 A_G4:C15_A A 4 ? A 15 ? 19 1 1 A G 5 1_555 A C 14 1_555 -0.090 -0.090 -0.338 -9.708 -11.189 -2.513 5 A_G5:C14_A A 5 ? A 14 ? 19 1 1 A G 6 1_555 A C 13 1_555 -0.297 -0.123 -0.096 -7.446 -6.900 -0.384 6 A_G6:C13_A A 6 ? A 13 ? 19 1 1 A G 7 1_555 A C 12 1_555 -0.181 -0.151 -0.159 -1.554 -1.318 -3.644 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 0.418 -1.932 3.211 0.834 2.502 28.314 -4.483 -0.668 3.043 5.100 -1.700 28.434 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 0.208 -1.608 3.208 -0.646 3.731 33.536 -3.347 -0.458 3.013 6.440 1.116 33.743 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 -0.421 -1.538 3.400 2.887 12.277 31.088 -4.591 1.183 2.577 21.815 -5.129 33.490 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 0.399 -1.873 3.368 0.856 10.402 28.100 -5.632 -0.608 2.539 20.548 -1.692 29.939 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 0.611 -1.933 3.254 1.315 4.537 28.940 -4.754 -0.937 2.947 9.003 -2.610 29.315 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 -0.073 -2.226 3.222 1.401 1.439 29.143 -4.717 0.440 3.104 2.856 -2.780 29.211 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 ? _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 5NEO _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 5NEQ _atom_sites.fract_transf_matrix[1][1] 0.018030 _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] 0.020819 _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] 0.007676 _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 NA O P S # loop_