data_5D8T # _entry.id 5D8T # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5D8T pdb_00005d8t 10.2210/pdb5d8t/pdb WWPDB D_1000212792 ? ? # 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 2016-06-29 2 'Structure model' 1 1 2016-07-27 3 'Structure model' 1 2 2024-03-06 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_oper_list # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5D8T _pdbx_database_status.recvd_initial_deposition_date 2015-08-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Harp, J.M.' 1 'Egli, M.' 2 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Org.Chem. _citation.journal_id_ASTM JOCEAH _citation.journal_id_CSD 0035 _citation.journal_id_ISSN 0022-3263 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 81 _citation.language ? _citation.page_first 2261 _citation.page_last 2279 _citation.title ;Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. ; _citation.year 2016 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.joc.5b02375 _citation.pdbx_database_id_PubMed 26940174 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kel In, A.V.' 1 ? primary 'Zlatev, I.' 2 ? primary 'Harp, J.' 3 ? primary 'Jayaraman, M.' 4 ? primary 'Bisbe, A.' 5 ? primary 'O Shea, J.' 6 ? primary 'Taneja, N.' 7 ? primary 'Manoharan, R.M.' 8 ? primary 'Khan, S.' 9 ? primary 'Charisse, K.' 10 ? primary 'Maier, M.A.' 11 ? primary 'Egli, M.' 12 ? primary 'Rajeev, K.G.' 13 ? primary 'Manoharan, M.' 14 ? # 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 oligonucleotide containing (S)-C5'-Me-2'-FU ; 2621.475 2 ? ? ? ? 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 4 ? ? ? ? 3 water nat water 18.015 126 ? ? ? ? # _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 '(CBV)GAA(U5M)UCG' _entity_poly.pdbx_seq_one_letter_code_can CGAAXUCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 CBV n 1 2 G n 1 3 A n 1 4 A n 1 5 U5M n 1 6 U n 1 7 C n 1 8 G 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 8 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 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 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 U5M 'RNA linking' . '1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione' ? 'C10 H14 F N2 O8 P' 340.199 # 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 CBV 1 1 1 CBV CBV A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 A 4 4 4 A A A . n A 1 5 U5M 5 5 5 U5M U5M A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n B 1 1 CBV 1 1 1 CBV CBV B . n B 1 2 G 2 2 2 G G B . n B 1 3 A 3 3 3 A A B . n B 1 4 A 4 4 4 A A B . n B 1 5 U5M 5 5 5 U5M U5M B . n B 1 6 U 6 6 6 U U B . n B 1 7 C 7 7 7 C C B . n B 1 8 G 8 8 8 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 NCO 1 101 101 NCO NCO A . D 2 NCO 1 102 102 NCO NCO A . E 2 NCO 1 101 101 NCO NCO B . F 2 NCO 1 102 102 NCO NCO B . G 3 HOH 1 201 201 HOH HOH A . G 3 HOH 2 202 202 HOH HOH A . G 3 HOH 3 203 203 HOH HOH A . G 3 HOH 4 204 204 HOH HOH A . G 3 HOH 5 205 205 HOH HOH A . G 3 HOH 6 206 206 HOH HOH A . G 3 HOH 7 207 207 HOH HOH A . G 3 HOH 8 208 208 HOH HOH A . G 3 HOH 9 209 209 HOH HOH A . G 3 HOH 10 210 210 HOH HOH A . G 3 HOH 11 211 211 HOH HOH A . G 3 HOH 12 212 212 HOH HOH A . G 3 HOH 13 213 213 HOH HOH A . G 3 HOH 14 214 214 HOH HOH A . G 3 HOH 15 215 215 HOH HOH A . G 3 HOH 16 216 216 HOH HOH A . G 3 HOH 17 217 217 HOH HOH A . G 3 HOH 18 218 218 HOH HOH A . G 3 HOH 19 219 219 HOH HOH A . G 3 HOH 20 220 220 HOH HOH A . G 3 HOH 21 221 221 HOH HOH A . G 3 HOH 22 222 222 HOH HOH A . G 3 HOH 23 223 223 HOH HOH A . G 3 HOH 24 224 224 HOH HOH A . G 3 HOH 25 225 225 HOH HOH A . G 3 HOH 26 226 226 HOH HOH A . G 3 HOH 27 227 227 HOH HOH A . G 3 HOH 28 228 228 HOH HOH A . G 3 HOH 29 229 229 HOH HOH A . G 3 HOH 30 230 230 HOH HOH A . G 3 HOH 31 231 231 HOH HOH A . G 3 HOH 32 232 232 HOH HOH A . G 3 HOH 33 233 233 HOH HOH A . G 3 HOH 34 234 234 HOH HOH A . G 3 HOH 35 235 235 HOH HOH A . G 3 HOH 36 236 236 HOH HOH A . G 3 HOH 37 237 237 HOH HOH A . G 3 HOH 38 238 238 HOH HOH A . G 3 HOH 39 239 239 HOH HOH A . G 3 HOH 40 240 240 HOH HOH A . G 3 HOH 41 241 241 HOH HOH A . G 3 HOH 42 242 242 HOH HOH A . G 3 HOH 43 243 243 HOH HOH A . G 3 HOH 44 244 244 HOH HOH A . G 3 HOH 45 245 245 HOH HOH A . G 3 HOH 46 246 246 HOH HOH A . G 3 HOH 47 247 247 HOH HOH A . G 3 HOH 48 248 248 HOH HOH A . G 3 HOH 49 249 249 HOH HOH A . G 3 HOH 50 250 250 HOH HOH A . G 3 HOH 51 251 251 HOH HOH A . G 3 HOH 52 252 252 HOH HOH A . G 3 HOH 53 253 253 HOH HOH A . G 3 HOH 54 254 254 HOH HOH A . G 3 HOH 55 255 255 HOH HOH A . G 3 HOH 56 256 256 HOH HOH A . G 3 HOH 57 257 257 HOH HOH A . G 3 HOH 58 258 258 HOH HOH A . G 3 HOH 59 259 259 HOH HOH A . H 3 HOH 1 201 201 HOH HOH B . H 3 HOH 2 202 202 HOH HOH B . H 3 HOH 3 203 203 HOH HOH B . H 3 HOH 4 204 204 HOH HOH B . H 3 HOH 5 205 205 HOH HOH B . H 3 HOH 6 206 206 HOH HOH B . H 3 HOH 7 207 207 HOH HOH B . H 3 HOH 8 208 208 HOH HOH B . H 3 HOH 9 209 209 HOH HOH B . H 3 HOH 10 210 210 HOH HOH B . H 3 HOH 11 211 211 HOH HOH B . H 3 HOH 12 212 212 HOH HOH B . H 3 HOH 13 213 213 HOH HOH B . H 3 HOH 14 214 214 HOH HOH B . H 3 HOH 15 215 215 HOH HOH B . H 3 HOH 16 216 216 HOH HOH B . H 3 HOH 17 217 217 HOH HOH B . H 3 HOH 18 218 218 HOH HOH B . H 3 HOH 19 219 219 HOH HOH B . H 3 HOH 20 220 220 HOH HOH B . H 3 HOH 21 221 221 HOH HOH B . H 3 HOH 22 222 222 HOH HOH B . H 3 HOH 23 223 223 HOH HOH B . H 3 HOH 24 224 224 HOH HOH B . H 3 HOH 25 225 225 HOH HOH B . H 3 HOH 26 226 226 HOH HOH B . H 3 HOH 27 227 227 HOH HOH B . H 3 HOH 28 228 228 HOH HOH B . H 3 HOH 29 229 229 HOH HOH B . H 3 HOH 30 230 230 HOH HOH B . H 3 HOH 31 231 231 HOH HOH B . H 3 HOH 32 232 232 HOH HOH B . H 3 HOH 33 233 233 HOH HOH B . H 3 HOH 34 234 234 HOH HOH B . H 3 HOH 35 235 235 HOH HOH B . H 3 HOH 36 236 236 HOH HOH B . H 3 HOH 37 237 237 HOH HOH B . H 3 HOH 38 238 238 HOH HOH B . H 3 HOH 39 239 239 HOH HOH B . H 3 HOH 40 240 240 HOH HOH B . H 3 HOH 41 241 241 HOH HOH B . H 3 HOH 42 242 242 HOH HOH B . H 3 HOH 43 243 243 HOH HOH B . H 3 HOH 44 244 244 HOH HOH B . H 3 HOH 45 245 245 HOH HOH B . H 3 HOH 46 246 246 HOH HOH B . H 3 HOH 47 247 247 HOH HOH B . H 3 HOH 48 248 248 HOH HOH B . H 3 HOH 49 249 249 HOH HOH B . H 3 HOH 50 250 250 HOH HOH B . H 3 HOH 51 251 251 HOH HOH B . H 3 HOH 52 252 252 HOH HOH B . H 3 HOH 53 253 253 HOH HOH B . H 3 HOH 54 254 254 HOH HOH B . H 3 HOH 55 255 255 HOH HOH B . H 3 HOH 56 256 256 HOH HOH B . H 3 HOH 57 257 257 HOH HOH B . H 3 HOH 58 258 258 HOH HOH B . H 3 HOH 59 259 259 HOH HOH B . H 3 HOH 60 260 260 HOH HOH B . H 3 HOH 61 261 261 HOH HOH B . H 3 HOH 62 262 262 HOH HOH B . H 3 HOH 63 263 263 HOH HOH B . H 3 HOH 64 264 264 HOH HOH B . H 3 HOH 65 265 265 HOH HOH B . H 3 HOH 66 266 266 HOH HOH B . H 3 HOH 67 267 267 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0073 1 ? 'data collection' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELX ? ? ? . 4 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.15 5 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 6 # _cell.entry_id 5D8T _cell.length_a 31.172 _cell.length_b 31.172 _cell.length_c 84.325 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5D8T _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # _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 5D8T _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.95 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 37.04 _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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '40 mM sodium cacodylate, 20 mM hexamine Co(III) chloride, 20 mM MgCl2' _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 'IMAGE PLATE' _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR scanner 300 mm plate' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-07-24 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91833 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 21-ID-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.91833 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 5D8T _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.000 _reflns.d_resolution_high 1.200 _reflns.number_obs 13758 _reflns.number_all ? _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.14500 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 11.3000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 14.10 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.20 _reflns_shell.d_res_low 1.22 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.58400 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 8.10 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 5D8T _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 12988 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.24 _refine.ls_d_res_high 1.20 _refine.ls_percent_reflns_obs 99.6 _refine.ls_R_factor_obs 0.121 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.120 _refine.ls_R_factor_R_free 0.157 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.200 _refine.ls_number_reflns_R_free 708 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.975 _refine.correlation_coeff_Fo_to_Fc_free 0.956 _refine.B_iso_mean 12.42 _refine.aniso_B[1][1] 0.00000 _refine.aniso_B[2][2] 0.00000 _refine.aniso_B[3][3] -0.01000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.035 _refine.pdbx_overall_ESU_R_Free 0.037 _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _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 338 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 126 _refine_hist.number_atoms_total 492 _refine_hist.d_res_high 1.20 _refine_hist.d_res_low 29.24 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 1.823 0.015 ? 252 'X-RAY DIFFRACTION' ? r_bond_other_d 2.887 0.018 ? 398 'X-RAY DIFFRACTION' ? r_angle_refined_deg 42.196 1.872 ? 303 'X-RAY DIFFRACTION' ? r_angle_other_deg 56.801 2.520 ? 891 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 3.623 0.200 ? 21 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.223 0.020 ? 156 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.296 0.020 ? 68 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 1.468 0.927 ? 252 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 14.638 3.000 ? 650 'X-RAY DIFFRACTION' ? r_sphericity_free 57.545 5.000 ? 15 'X-RAY DIFFRACTION' ? r_sphericity_bonded 7.632 5.000 ? 731 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.20 _refine_ls_shell.d_res_low 1.23 _refine_ls_shell.number_reflns_R_work 900 _refine_ls_shell.R_factor_R_work 0.1400 _refine_ls_shell.percent_reflns_obs 98.44 _refine_ls_shell.R_factor_R_free 0.1610 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 46 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 5D8T _struct.title ;RNA octamer containing (S)-5' methyl, 2'-F U. ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5D8T _struct_keywords.text 'RNA, modified base' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5D8T _struct_ref.pdbx_db_accession 5D8T _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5D8T A 1 ? 8 ? 5D8T 1 ? 8 ? 1 8 2 1 5D8T B 1 ? 8 ? 5D8T 1 ? 8 ? 1 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2350 ? 1 MORE -1 ? 1 'SSA (A^2)' 3160 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A CBV 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A CBV 1 A G 2 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale2 covale both ? A A 4 "O3'" ? ? ? 1_555 A U5M 5 P ? ? A A 4 A U5M 5 1_555 ? ? ? ? ? ? ? 1.642 ? ? covale3 covale one ? A U5M 5 "O3'" ? ? ? 1_555 A U 6 P ? ? A U5M 5 A U 6 1_555 ? ? ? ? ? ? ? 1.581 ? ? covale4 covale one ? B CBV 1 "O3'" ? ? ? 1_555 B G 2 P ? ? B CBV 1 B G 2 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale5 covale both ? B A 4 "O3'" ? ? ? 1_555 B U5M 5 P ? ? B A 4 B U5M 5 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale6 covale one ? B U5M 5 "O3'" ? ? ? 1_555 B U 6 P ? ? B U5M 5 B U 6 1_555 ? ? ? ? ? ? ? 1.563 ? ? hydrog1 hydrog ? ? A CBV 1 N3 ? ? ? 1_555 B G 8 N1 ? ? A CBV 1 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A CBV 1 N4 ? ? ? 1_555 B G 8 O6 ? ? A CBV 1 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A CBV 1 O2 ? ? ? 1_555 B G 8 N2 ? ? A CBV 1 B G 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 2 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 3 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 3 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 6 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 6 B A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 7 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 7 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 7 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 8 N1 ? ? ? 1_555 B CBV 1 N3 ? ? A G 8 B CBV 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 8 N2 ? ? ? 1_555 B CBV 1 O2 ? ? A G 8 B CBV 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 O6 ? ? ? 1_555 B CBV 1 N4 ? ? A G 8 B CBV 1 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 NCO 101 ? 10 'binding site for residue NCO A 101' AC2 Software A NCO 102 ? 10 'binding site for residue NCO A 102' AC3 Software B NCO 101 ? 12 'binding site for residue NCO B 101' AC4 Software B NCO 102 ? 6 'binding site for residue NCO B 102' AC5 Software B CBV 1 ? 21 'binding site for Di-nucleotide CBV B 1 and G B 2' AC6 Software B A 4 ? 25 'binding site for Di-nucleotide A B 4 and U5M B 5' # 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 10 A A 3 ? A A 3 . ? 1_555 ? 2 AC1 10 U5M A 5 ? U5M A 5 . ? 1_555 ? 3 AC1 10 U A 6 ? U A 6 . ? 1_555 ? 4 AC1 10 HOH G . ? HOH A 220 . ? 1_555 ? 5 AC1 10 HOH G . ? HOH A 223 . ? 1_555 ? 6 AC1 10 HOH G . ? HOH A 230 . ? 1_555 ? 7 AC1 10 HOH G . ? HOH A 236 . ? 1_555 ? 8 AC1 10 HOH G . ? HOH A 237 . ? 1_555 ? 9 AC1 10 HOH H . ? HOH B 222 . ? 1_555 ? 10 AC1 10 HOH H . ? HOH B 244 . ? 4_545 ? 11 AC2 10 CBV A 1 ? CBV A 1 . ? 6_535 ? 12 AC2 10 G A 2 ? G A 2 . ? 6_535 ? 13 AC2 10 A A 4 ? A A 4 . ? 1_555 ? 14 AC2 10 U5M A 5 ? U5M A 5 . ? 1_555 ? 15 AC2 10 HOH G . ? HOH A 240 . ? 1_555 ? 16 AC2 10 HOH G . ? HOH A 256 . ? 6_535 ? 17 AC2 10 HOH H . ? HOH B 245 . ? 6_535 ? 18 AC2 10 HOH H . ? HOH B 248 . ? 4_545 ? 19 AC2 10 HOH H . ? HOH B 252 . ? 6_535 ? 20 AC2 10 HOH H . ? HOH B 261 . ? 4_545 ? 21 AC3 12 CBV A 1 ? CBV A 1 . ? 1_555 ? 22 AC3 12 G A 2 ? G A 2 . ? 1_555 ? 23 AC3 12 HOH G . ? HOH A 215 . ? 1_555 ? 24 AC3 12 HOH G . ? HOH A 238 . ? 1_555 ? 25 AC3 12 HOH G . ? HOH A 246 . ? 3_444 ? 26 AC3 12 G B 2 ? G B 2 . ? 1_555 ? 27 AC3 12 A B 3 ? A B 3 . ? 1_555 ? 28 AC3 12 HOH H . ? HOH B 225 . ? 1_555 ? 29 AC3 12 HOH H . ? HOH B 229 . ? 1_555 ? 30 AC3 12 HOH H . ? HOH B 230 . ? 1_555 ? 31 AC3 12 HOH H . ? HOH B 241 . ? 1_555 ? 32 AC3 12 HOH H . ? HOH B 247 . ? 1_555 ? 33 AC4 6 C A 7 ? C A 7 . ? 3_444 ? 34 AC4 6 G A 8 ? G A 8 . ? 3_444 ? 35 AC4 6 HOH G . ? HOH A 224 . ? 3_444 ? 36 AC4 6 HOH G . ? HOH A 255 . ? 3_444 ? 37 AC4 6 A B 4 ? A B 4 . ? 1_555 ? 38 AC4 6 HOH H . ? HOH B 215 . ? 1_555 ? 39 AC5 21 A A 4 ? A A 4 . ? 6_435 ? 40 AC5 21 C A 7 ? C A 7 . ? 1_555 ? 41 AC5 21 G A 8 ? G A 8 . ? 1_555 ? 42 AC5 21 HOH G . ? HOH A 242 . ? 6_435 ? 43 AC5 21 A B 3 ? A B 3 . ? 1_555 ? 44 AC5 21 G B 8 ? G B 8 . ? 4_545 ? 45 AC5 21 NCO E . ? NCO B 101 . ? 1_555 ? 46 AC5 21 HOH H . ? HOH B 203 . ? 1_555 ? 47 AC5 21 HOH H . ? HOH B 204 . ? 1_555 ? 48 AC5 21 HOH H . ? HOH B 217 . ? 1_555 ? 49 AC5 21 HOH H . ? HOH B 218 . ? 1_555 ? 50 AC5 21 HOH H . ? HOH B 219 . ? 1_555 ? 51 AC5 21 HOH H . ? HOH B 221 . ? 1_555 ? 52 AC5 21 HOH H . ? HOH B 222 . ? 1_555 ? 53 AC5 21 HOH H . ? HOH B 232 . ? 1_555 ? 54 AC5 21 HOH H . ? HOH B 234 . ? 1_555 ? 55 AC5 21 HOH H . ? HOH B 236 . ? 1_555 ? 56 AC5 21 HOH H . ? HOH B 241 . ? 1_555 ? 57 AC5 21 HOH H . ? HOH B 244 . ? 4_545 ? 58 AC5 21 HOH H . ? HOH B 245 . ? 1_555 ? 59 AC5 21 HOH H . ? HOH B 249 . ? 1_555 ? 60 AC6 25 A A 4 ? A A 4 . ? 1_555 ? 61 AC6 25 U5M A 5 ? U5M A 5 . ? 1_555 ? 62 AC6 25 U A 6 ? U A 6 . ? 6_445 ? 63 AC6 25 U A 6 ? U A 6 . ? 1_555 ? 64 AC6 25 HOH G . ? HOH A 211 . ? 6_545 ? 65 AC6 25 HOH G . ? HOH A 227 . ? 6_445 ? 66 AC6 25 HOH G . ? HOH A 237 . ? 1_555 ? 67 AC6 25 HOH G . ? HOH A 251 . ? 6_545 ? 68 AC6 25 HOH G . ? HOH A 255 . ? 3_444 ? 69 AC6 25 A B 3 ? A B 3 . ? 1_555 ? 70 AC6 25 U B 6 ? U B 6 . ? 1_555 ? 71 AC6 25 NCO F . ? NCO B 102 . ? 1_555 ? 72 AC6 25 HOH H . ? HOH B 206 . ? 1_555 ? 73 AC6 25 HOH H . ? HOH B 207 . ? 1_555 ? 74 AC6 25 HOH H . ? HOH B 208 . ? 1_555 ? 75 AC6 25 HOH H . ? HOH B 214 . ? 1_555 ? 76 AC6 25 HOH H . ? HOH B 216 . ? 1_555 ? 77 AC6 25 HOH H . ? HOH B 224 . ? 1_555 ? 78 AC6 25 HOH H . ? HOH B 225 . ? 1_555 ? 79 AC6 25 HOH H . ? HOH B 226 . ? 1_555 ? 80 AC6 25 HOH H . ? HOH B 227 . ? 1_555 ? 81 AC6 25 HOH H . ? HOH B 230 . ? 1_555 ? 82 AC6 25 HOH H . ? HOH B 237 . ? 1_555 ? 83 AC6 25 HOH H . ? HOH B 240 . ? 1_555 ? 84 AC6 25 HOH H . ? HOH B 243 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O B HOH 212 ? ? O B HOH 261 ? ? 1.71 2 1 O B HOH 201 ? ? O B HOH 212 ? ? 1.95 3 1 O B HOH 243 ? ? O B HOH 263 ? ? 2.12 # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 A A 3 ? ? 0.065 'SIDE CHAIN' 2 1 G B 8 ? ? 0.060 'SIDE CHAIN' # _diffrn_reflns.diffrn_id 1 _diffrn_reflns.pdbx_d_res_high 1.200 _diffrn_reflns.pdbx_d_res_low 50.000 _diffrn_reflns.pdbx_number_obs 13758 _diffrn_reflns.pdbx_Rmerge_I_obs 0.145 _diffrn_reflns.pdbx_Rsym_value ? _diffrn_reflns.pdbx_chi_squared 1.09 _diffrn_reflns.pdbx_redundancy 14.10 _diffrn_reflns.pdbx_rejects ? _diffrn_reflns.pdbx_percent_possible_obs 99.70 _diffrn_reflns.pdbx_observed_criterion ? _diffrn_reflns.number 193718 _diffrn_reflns.limit_h_max ? _diffrn_reflns.limit_h_min ? _diffrn_reflns.limit_k_max ? _diffrn_reflns.limit_k_min ? _diffrn_reflns.limit_l_max ? _diffrn_reflns.limit_l_min ? # loop_ _pdbx_diffrn_reflns_shell.diffrn_id _pdbx_diffrn_reflns_shell.d_res_high _pdbx_diffrn_reflns_shell.d_res_low _pdbx_diffrn_reflns_shell.number_obs _pdbx_diffrn_reflns_shell.rejects _pdbx_diffrn_reflns_shell.Rmerge_I_obs _pdbx_diffrn_reflns_shell.Rsym_value _pdbx_diffrn_reflns_shell.chi_squared _pdbx_diffrn_reflns_shell.redundancy _pdbx_diffrn_reflns_shell.percent_possible_obs 1 3.26 50.00 ? ? 0.074 ? 1.029 13.10 ? 1 2.59 3.26 ? ? 0.088 ? 1.074 15.20 ? 1 2.26 2.59 ? ? 0.103 ? 1.253 16.40 ? 1 2.05 2.26 ? ? 0.123 ? 1.259 16.50 ? 1 1.90 2.05 ? ? 0.137 ? 1.152 16.70 ? 1 1.79 1.90 ? ? 0.157 ? 1.132 16.70 ? 1 1.70 1.79 ? ? 0.168 ? 1.123 16.90 ? 1 1.63 1.70 ? ? 0.214 ? 1.177 16.70 ? 1 1.57 1.63 ? ? 0.303 ? 1.118 16.90 ? 1 1.51 1.57 ? ? 0.391 ? 1.127 16.60 ? 1 1.46 1.51 ? ? 0.510 ? 1.086 16.40 ? 1 1.42 1.46 ? ? 0.555 ? 1.033 16.00 ? 1 1.39 1.42 ? ? 0.589 ? 1.056 14.70 ? 1 1.35 1.39 ? ? 0.577 ? 1.006 13.00 ? 1 1.32 1.35 ? ? 0.500 ? 1.047 11.70 ? 1 1.29 1.32 ? ? 0.534 ? 1.000 11.10 ? 1 1.27 1.29 ? ? 0.498 ? 0.997 10.10 ? 1 1.24 1.27 ? ? 0.529 ? 0.933 9.40 ? 1 1.22 1.24 ? ? 0.552 ? 0.937 8.70 ? 1 1.20 1.22 ? ? 0.584 ? 0.953 8.10 ? # _phasing.method SAD # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 257 ? 6.42 . 2 1 O ? A HOH 258 ? 6.78 . 3 1 O ? A HOH 259 ? 7.04 . 4 1 O ? B HOH 267 ? 6.56 . # 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 G OP3 O N N 108 G P P N N 109 G OP1 O N N 110 G OP2 O N N 111 G "O5'" O N N 112 G "C5'" C N N 113 G "C4'" C N R 114 G "O4'" O N N 115 G "C3'" C N S 116 G "O3'" O N N 117 G "C2'" C N R 118 G "O2'" O N N 119 G "C1'" C N R 120 G N9 N Y N 121 G C8 C Y N 122 G N7 N Y N 123 G C5 C Y N 124 G C6 C N N 125 G O6 O N N 126 G N1 N N N 127 G C2 C N N 128 G N2 N N N 129 G N3 N N N 130 G C4 C Y N 131 G HOP3 H N N 132 G HOP2 H N N 133 G "H5'" H N N 134 G "H5''" H N N 135 G "H4'" H N N 136 G "H3'" H N N 137 G "HO3'" H N N 138 G "H2'" H N N 139 G "HO2'" H N N 140 G "H1'" H N N 141 G H8 H N N 142 G H1 H N N 143 G H21 H N N 144 G H22 H N N 145 HOH O O N N 146 HOH H1 H N N 147 HOH H2 H N N 148 NCO CO CO N N 149 NCO N1 N N N 150 NCO N2 N N N 151 NCO N3 N N N 152 NCO N4 N N N 153 NCO N5 N N N 154 NCO N6 N N N 155 NCO HN11 H N N 156 NCO HN12 H N N 157 NCO HN13 H N N 158 NCO HN21 H N N 159 NCO HN22 H N N 160 NCO HN23 H N N 161 NCO HN31 H N N 162 NCO HN32 H N N 163 NCO HN33 H N N 164 NCO HN41 H N N 165 NCO HN42 H N N 166 NCO HN43 H N N 167 NCO HN51 H N N 168 NCO HN52 H N N 169 NCO HN53 H N N 170 NCO HN61 H N N 171 NCO HN62 H N N 172 NCO HN63 H N N 173 U OP3 O N N 174 U P P N N 175 U OP1 O N N 176 U OP2 O N N 177 U "O5'" O N N 178 U "C5'" C N N 179 U "C4'" C N R 180 U "O4'" O N N 181 U "C3'" C N S 182 U "O3'" O N N 183 U "C2'" C N R 184 U "O2'" O N N 185 U "C1'" C N R 186 U N1 N N N 187 U C2 C N N 188 U O2 O N N 189 U N3 N N N 190 U C4 C N N 191 U O4 O N N 192 U C5 C N N 193 U C6 C N N 194 U HOP3 H N N 195 U HOP2 H N N 196 U "H5'" H N N 197 U "H5''" H N N 198 U "H4'" H N N 199 U "H3'" H N N 200 U "HO3'" H N N 201 U "H2'" H N N 202 U "HO2'" H N N 203 U "H1'" H N N 204 U H3 H N N 205 U H5 H N N 206 U H6 H N N 207 U5M O2 O N N 208 U5M C2 C N N 209 U5M N3 N N N 210 U5M C4 C N N 211 U5M O4 O N N 212 U5M C5 C N N 213 U5M C6 C N N 214 U5M N1 N N N 215 U5M "C1'" C N R 216 U5M "O4'" O N N 217 U5M "C2'" C N R 218 U5M "F2'" F N N 219 U5M "C3'" C N R 220 U5M "O3'" O N N 221 U5M "C4'" C N S 222 U5M "C5'" C N S 223 U5M C5M C N N 224 U5M "O5'" O N N 225 U5M P P N N 226 U5M OP1 O N N 227 U5M OP2 O N N 228 U5M H3 H N N 229 U5M H5 H N N 230 U5M H6 H N N 231 U5M "H1'" H N N 232 U5M "H2'" H N N 233 U5M "H3'" H N N 234 U5M H6N H N N 235 U5M "H4'" H N N 236 U5M "H5'" H N N 237 U5M H6L H N N 238 U5M H6M H N N 239 U5M H5M H N N 240 U5M H1 H N N 241 U5M OP3 O N N 242 U5M H2 H N N 243 # 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 G OP3 P sing N N 112 G OP3 HOP3 sing N N 113 G P OP1 doub N N 114 G P OP2 sing N N 115 G P "O5'" sing N N 116 G OP2 HOP2 sing N N 117 G "O5'" "C5'" sing N N 118 G "C5'" "C4'" sing N N 119 G "C5'" "H5'" sing N N 120 G "C5'" "H5''" sing N N 121 G "C4'" "O4'" sing N N 122 G "C4'" "C3'" sing N N 123 G "C4'" "H4'" sing N N 124 G "O4'" "C1'" sing N N 125 G "C3'" "O3'" sing N N 126 G "C3'" "C2'" sing N N 127 G "C3'" "H3'" sing N N 128 G "O3'" "HO3'" sing N N 129 G "C2'" "O2'" sing N N 130 G "C2'" "C1'" sing N N 131 G "C2'" "H2'" sing N N 132 G "O2'" "HO2'" sing N N 133 G "C1'" N9 sing N N 134 G "C1'" "H1'" sing N N 135 G N9 C8 sing Y N 136 G N9 C4 sing Y N 137 G C8 N7 doub Y N 138 G C8 H8 sing N N 139 G N7 C5 sing Y N 140 G C5 C6 sing N N 141 G C5 C4 doub Y N 142 G C6 O6 doub N N 143 G C6 N1 sing N N 144 G N1 C2 sing N N 145 G N1 H1 sing N N 146 G C2 N2 sing N N 147 G C2 N3 doub N N 148 G N2 H21 sing N N 149 G N2 H22 sing N N 150 G N3 C4 sing N N 151 HOH O H1 sing N N 152 HOH O H2 sing N N 153 NCO CO N1 sing N N 154 NCO CO N2 sing N N 155 NCO CO N3 sing N N 156 NCO CO N4 sing N N 157 NCO CO N5 sing N N 158 NCO CO N6 sing N N 159 NCO N1 HN11 sing N N 160 NCO N1 HN12 sing N N 161 NCO N1 HN13 sing N N 162 NCO N2 HN21 sing N N 163 NCO N2 HN22 sing N N 164 NCO N2 HN23 sing N N 165 NCO N3 HN31 sing N N 166 NCO N3 HN32 sing N N 167 NCO N3 HN33 sing N N 168 NCO N4 HN41 sing N N 169 NCO N4 HN42 sing N N 170 NCO N4 HN43 sing N N 171 NCO N5 HN51 sing N N 172 NCO N5 HN52 sing N N 173 NCO N5 HN53 sing N N 174 NCO N6 HN61 sing N N 175 NCO N6 HN62 sing N N 176 NCO N6 HN63 sing N N 177 U OP3 P sing N N 178 U OP3 HOP3 sing N N 179 U P OP1 doub N N 180 U P OP2 sing N N 181 U P "O5'" sing N N 182 U OP2 HOP2 sing N N 183 U "O5'" "C5'" sing N N 184 U "C5'" "C4'" sing N N 185 U "C5'" "H5'" sing N N 186 U "C5'" "H5''" sing N N 187 U "C4'" "O4'" sing N N 188 U "C4'" "C3'" sing N N 189 U "C4'" "H4'" sing N N 190 U "O4'" "C1'" sing N N 191 U "C3'" "O3'" sing N N 192 U "C3'" "C2'" sing N N 193 U "C3'" "H3'" sing N N 194 U "O3'" "HO3'" sing N N 195 U "C2'" "O2'" sing N N 196 U "C2'" "C1'" sing N N 197 U "C2'" "H2'" sing N N 198 U "O2'" "HO2'" sing N N 199 U "C1'" N1 sing N N 200 U "C1'" "H1'" sing N N 201 U N1 C2 sing N N 202 U N1 C6 sing N N 203 U C2 O2 doub N N 204 U C2 N3 sing N N 205 U N3 C4 sing N N 206 U N3 H3 sing N N 207 U C4 O4 doub N N 208 U C4 C5 sing N N 209 U C5 C6 doub N N 210 U C5 H5 sing N N 211 U C6 H6 sing N N 212 U5M O2 C2 doub N N 213 U5M C2 N3 sing N N 214 U5M C2 N1 sing N N 215 U5M N3 C4 sing N N 216 U5M C4 O4 doub N N 217 U5M C4 C5 sing N N 218 U5M C5 C6 doub N N 219 U5M C6 N1 sing N N 220 U5M N1 "C1'" sing N N 221 U5M "C1'" "O4'" sing N N 222 U5M "C1'" "C2'" sing N N 223 U5M "O4'" "C4'" sing N N 224 U5M "C2'" "F2'" sing N N 225 U5M "C2'" "C3'" sing N N 226 U5M "C3'" "O3'" sing N N 227 U5M "C3'" "C4'" sing N N 228 U5M "C4'" "C5'" sing N N 229 U5M "C5'" C5M sing N N 230 U5M "C5'" "O5'" sing N N 231 U5M "O5'" P sing N N 232 U5M P OP1 doub N N 233 U5M P OP2 sing N N 234 U5M N3 H3 sing N N 235 U5M C5 H5 sing N N 236 U5M C6 H6 sing N N 237 U5M "C1'" "H1'" sing N N 238 U5M "C2'" "H2'" sing N N 239 U5M "C3'" "H3'" sing N N 240 U5M "O3'" H6N sing N N 241 U5M "C4'" "H4'" sing N N 242 U5M "C5'" "H5'" sing N N 243 U5M C5M H6L sing N N 244 U5M C5M H6M sing N N 245 U5M C5M H5M sing N N 246 U5M OP2 H1 sing N N 247 U5M P OP3 sing N N 248 U5M OP3 H2 sing N N 249 # _ndb_struct_conf_na.entry_id 5D8T _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A CBV 1 1_555 B G 8 1_555 0.123 -0.086 -0.143 7.111 -8.572 -1.296 1 A_CBV1:G8_B A 1 ? B 8 ? 19 1 1 A G 2 1_555 B C 7 1_555 -0.227 -0.175 0.047 -4.494 -19.164 -0.597 2 A_G2:C7_B A 2 ? B 7 ? 19 1 1 A A 3 1_555 B U 6 1_555 0.032 -0.089 -0.181 -8.964 -11.426 -3.091 3 A_A3:U6_B A 3 ? B 6 ? 20 1 1 A U 6 1_555 B A 3 1_555 -0.024 -0.098 0.044 3.342 -14.179 3.453 4 A_U6:A3_B A 6 ? B 3 ? 20 1 1 A C 7 1_555 B G 2 1_555 0.252 -0.163 -0.017 1.039 -14.459 0.047 5 A_C7:G2_B A 7 ? B 2 ? 19 1 1 A G 8 1_555 B CBV 1 1_555 -0.177 -0.126 -0.090 -9.355 -14.546 -0.813 6 A_G8:CBV1_B A 8 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A CBV 1 1_555 B G 8 1_555 A G 2 1_555 B C 7 1_555 0.313 -1.801 3.425 -1.757 12.864 34.285 -4.552 -0.728 2.587 20.915 2.857 36.591 1 AA_CBV1G2:C7G8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A G 2 1_555 B C 7 1_555 A A 3 1_555 B U 6 1_555 -0.963 -1.560 3.309 0.153 6.938 35.466 -3.464 1.574 2.957 11.256 -0.248 36.117 2 AA_G2A3:U6C7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A U 6 1_555 B A 3 1_555 A C 7 1_555 B G 2 1_555 -0.342 -1.479 3.257 -0.524 6.714 32.819 -3.621 0.511 2.911 11.729 0.915 33.484 3 AA_U6C7:G2A3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A C 7 1_555 B G 2 1_555 A G 8 1_555 B CBV 1 1_555 0.133 -1.704 3.356 2.033 14.784 30.751 -5.056 0.068 2.322 26.043 -3.582 34.102 4 AA_C7G8:CBV1G2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _atom_sites.entry_id 5D8T _atom_sites.fract_transf_matrix[1][1] 0.032080 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032080 _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] 0.011859 _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 CO F H N O P # loop_