data_5IX7 # _entry.id 5IX7 # _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 5IX7 pdb_00005ix7 10.2210/pdb5ix7/pdb WWPDB D_1000219413 ? ? # 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 2017-07-05 2 'Structure model' 1 1 2017-10-11 3 'Structure model' 1 2 2024-03-20 # _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' '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 2 'Structure model' citation 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 '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_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.journal_volume' 6 2 'Structure model' '_citation.page_first' 7 2 'Structure model' '_citation.page_last' 8 2 'Structure model' '_citation.pdbx_database_id_DOI' 9 2 'Structure model' '_citation.pdbx_database_id_PubMed' 10 2 'Structure model' '_citation.year' 11 3 'Structure model' '_database_2.pdbx_DOI' 12 3 'Structure model' '_database_2.pdbx_database_accession' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 17 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 18 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 19 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 20 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 21 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 22 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 23 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 24 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 25 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 26 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 27 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 28 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 29 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 30 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 31 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 32 3 'Structure model' '_pdbx_struct_conn_angle.value' 33 3 'Structure model' '_struct_conn.conn_type_id' 34 3 'Structure model' '_struct_conn.id' 35 3 'Structure model' '_struct_conn.pdbx_dist_value' 36 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 37 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 38 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 39 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 40 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 41 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 42 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 43 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 44 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 45 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 46 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 47 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 48 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 49 3 'Structure model' '_struct_conn.ptnr2_symmetry' 50 3 '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 5IX7 _pdbx_database_status.recvd_initial_deposition_date 2016-03-23 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 'Kondo, J.' 1 ? 'Tada, Y.' 2 ? 'Dairaku, T.' 3 ? 'Hattori, Y.' 4 ? 'Saneyoshi, H.' 5 ? 'Ono, A.' 6 ? 'Tanaka, Y.' 7 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Chem' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1755-4349 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 9 _citation.language ? _citation.page_first 956 _citation.page_last 960 _citation.title 'A metallo-DNA nanowire with uninterrupted one-dimensional silver array' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/nchem.2808 _citation.pdbx_database_id_PubMed 28937663 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Tada, Y.' 2 ? primary 'Dairaku, T.' 3 ? primary 'Hattori, Y.' 4 ? primary 'Saneyoshi, H.' 5 ? primary 'Ono, A.' 6 ? primary 'Tanaka, Y.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*GP*AP*CP*TP*(CBR)P*GP*AP*CP*TP*CP*C)-3') ; 3702.264 1 ? ? ? ? 2 non-polymer syn 'SILVER ION' 107.868 6 ? ? ? ? 3 non-polymer syn 'POTASSIUM ION' 39.098 2 ? ? ? ? 4 water nat water 18.015 88 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DA)(DC)(DT)(CBR)(DG)(DA)(DC)(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GGACTCGACTCC _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 'SILVER ION' AG 3 'POTASSIUM ION' K 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DA n 1 4 DC n 1 5 DT n 1 6 CBR n 1 7 DG n 1 8 DA n 1 9 DC n 1 10 DT n 1 11 DC n 1 12 DC 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 12 _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 AG non-polymer . 'SILVER ION' ? 'Ag 1' 107.868 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 # 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 DG 1 1 1 DG DG A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 CBR 6 6 6 CBR CB2 A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DC 12 12 12 DC DC 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 AG 1 101 51 AG AG A . C 2 AG 1 102 52 AG AG A . D 2 AG 1 103 53 AG AG A . E 2 AG 1 104 54 AG AG A . F 2 AG 1 105 55 AG AG A . G 2 AG 1 106 56 AG AG A . H 3 K 1 107 61 K K A . I 3 K 1 108 62 K K A . J 4 HOH 1 201 101 HOH HOH A . J 4 HOH 2 202 212 HOH HOH A . J 4 HOH 3 203 139 HOH HOH A . J 4 HOH 4 204 103 HOH HOH A . J 4 HOH 5 205 110 HOH HOH A . J 4 HOH 6 206 157 HOH HOH A . J 4 HOH 7 207 188 HOH HOH A . J 4 HOH 8 208 175 HOH HOH A . J 4 HOH 9 209 131 HOH HOH A . J 4 HOH 10 210 191 HOH HOH A . J 4 HOH 11 211 102 HOH HOH A . J 4 HOH 12 212 164 HOH HOH A . J 4 HOH 13 213 128 HOH HOH A . J 4 HOH 14 214 221 HOH HOH A . J 4 HOH 15 215 275 HOH HOH A . J 4 HOH 16 216 155 HOH HOH A . J 4 HOH 17 217 105 HOH HOH A . J 4 HOH 18 218 126 HOH HOH A . J 4 HOH 19 219 192 HOH HOH A . J 4 HOH 20 220 107 HOH HOH A . J 4 HOH 21 221 108 HOH HOH A . J 4 HOH 22 222 122 HOH HOH A . J 4 HOH 23 223 129 HOH HOH A . J 4 HOH 24 224 130 HOH HOH A . J 4 HOH 25 225 104 HOH HOH A . J 4 HOH 26 226 133 HOH HOH A . J 4 HOH 27 227 163 HOH HOH A . J 4 HOH 28 228 135 HOH HOH A . J 4 HOH 29 229 106 HOH HOH A . J 4 HOH 30 230 109 HOH HOH A . J 4 HOH 31 231 111 HOH HOH A . J 4 HOH 32 232 119 HOH HOH A . J 4 HOH 33 233 174 HOH HOH A . J 4 HOH 34 234 138 HOH HOH A . J 4 HOH 35 235 158 HOH HOH A . J 4 HOH 36 236 273 HOH HOH A . J 4 HOH 37 237 214 HOH HOH A . J 4 HOH 38 238 153 HOH HOH A . J 4 HOH 39 239 137 HOH HOH A . J 4 HOH 40 240 242 HOH HOH A . J 4 HOH 41 241 125 HOH HOH A . J 4 HOH 42 242 140 HOH HOH A . J 4 HOH 43 243 190 HOH HOH A . J 4 HOH 44 244 181 HOH HOH A . J 4 HOH 45 245 143 HOH HOH A . J 4 HOH 46 246 238 HOH HOH A . J 4 HOH 47 247 136 HOH HOH A . J 4 HOH 48 248 114 HOH HOH A . J 4 HOH 49 249 161 HOH HOH A . J 4 HOH 50 250 134 HOH HOH A . J 4 HOH 51 251 146 HOH HOH A . J 4 HOH 52 252 149 HOH HOH A . J 4 HOH 53 253 144 HOH HOH A . J 4 HOH 54 254 116 HOH HOH A . J 4 HOH 55 255 132 HOH HOH A . J 4 HOH 56 256 243 HOH HOH A . J 4 HOH 57 257 117 HOH HOH A . J 4 HOH 58 258 118 HOH HOH A . J 4 HOH 59 259 178 HOH HOH A . J 4 HOH 60 260 169 HOH HOH A . J 4 HOH 61 261 196 HOH HOH A . J 4 HOH 62 262 177 HOH HOH A . J 4 HOH 63 263 219 HOH HOH A . J 4 HOH 64 264 172 HOH HOH A . J 4 HOH 65 265 165 HOH HOH A . J 4 HOH 66 266 274 HOH HOH A . J 4 HOH 67 267 113 HOH HOH A . J 4 HOH 68 268 120 HOH HOH A . J 4 HOH 69 269 115 HOH HOH A . J 4 HOH 70 270 235 HOH HOH A . J 4 HOH 71 271 127 HOH HOH A . J 4 HOH 72 272 222 HOH HOH A . J 4 HOH 73 273 241 HOH HOH A . J 4 HOH 74 274 167 HOH HOH A . J 4 HOH 75 275 218 HOH HOH A . J 4 HOH 76 276 270 HOH HOH A . J 4 HOH 77 277 262 HOH HOH A . J 4 HOH 78 278 248 HOH HOH A . J 4 HOH 79 279 227 HOH HOH A . J 4 HOH 80 280 260 HOH HOH A . J 4 HOH 81 281 230 HOH HOH A . J 4 HOH 82 282 228 HOH HOH A . J 4 HOH 83 283 259 HOH HOH A . J 4 HOH 84 284 232 HOH HOH A . J 4 HOH 85 285 203 HOH HOH A . J 4 HOH 86 286 231 HOH HOH A . J 4 HOH 87 287 234 HOH HOH A . J 4 HOH 88 288 200 HOH HOH A . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.6.4_486 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.20 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 5 # _cell.length_a 30.150 _cell.length_b 30.150 _cell.length_c 118.420 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 5IX7 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.entry_id 5IX7 _symmetry.Int_Tables_number 178 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # _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 5IX7 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.10 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 41.38 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 7.0 _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 'MOPS (pH 7.0), Spermine, MPD, KNO3' _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 EIGER X 4M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2015-05-25 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.1 _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 'PHOTON FACTORY BEAMLINE BL-1A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-1A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.entry_id 5IX7 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 26.111 _reflns.d_resolution_high 1.400 _reflns.number_obs 11942 _reflns.number_all ? _reflns.percent_possible_obs 100.000 _reflns.pdbx_Rmerge_I_obs 0.075 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 19.680 _reflns.B_iso_Wilson_estimate 10.160 _reflns.pdbx_redundancy 10.020 _reflns.pdbx_Rrim_I_all 0.079 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_CC_half 0.998 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_number_measured_all 119653 _reflns.pdbx_scaling_rejects 0 _reflns.pdbx_chi_squared 1.169 _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.details ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_CC_half 1 1 1.400 1.430 8410 ? 907 ? 0.284 6.950 ? ? 9.272 ? ? 905 ? ? ? ? ? 100.000 0.301 ? 0.947 1 2 1.430 1.470 8801 ? 840 ? 0.219 9.690 ? ? 10.477 ? ? 840 ? ? ? ? ? 100.000 0.231 ? 0.971 1 3 1.470 1.520 8871 ? 845 ? 0.173 11.740 ? ? 10.498 ? ? 845 ? ? ? ? ? 100.000 0.182 ? 0.988 1 4 1.520 1.560 8492 ? 801 ? 0.174 11.750 ? ? 10.602 ? ? 801 ? ? ? ? ? 100.000 0.183 ? 0.988 1 5 1.560 1.610 8343 ? 784 ? 0.156 13.620 ? ? 10.642 ? ? 784 ? ? ? ? ? 100.000 0.165 ? 0.984 1 6 1.610 1.670 8281 ? 788 ? 0.139 15.770 ? ? 10.509 ? ? 788 ? ? ? ? ? 100.000 0.146 ? 0.985 1 7 1.670 1.730 7498 ? 718 ? 0.123 18.470 ? ? 10.443 ? ? 718 ? ? ? ? ? 100.000 0.129 ? 0.990 1 8 1.730 1.800 7441 ? 714 ? 0.113 19.630 ? ? 10.422 ? ? 714 ? ? ? ? ? 100.000 0.119 ? 0.993 1 9 1.800 1.880 7068 ? 683 ? 0.104 21.030 ? ? 10.348 ? ? 683 ? ? ? ? ? 100.000 0.110 ? 0.993 1 10 1.880 1.980 6471 ? 633 ? 0.097 22.710 ? ? 10.223 ? ? 633 ? ? ? ? ? 100.000 0.102 ? 0.994 1 11 1.980 2.080 6211 ? 616 ? 0.086 24.260 ? ? 10.083 ? ? 616 ? ? ? ? ? 100.000 0.091 ? 0.995 1 12 2.080 2.210 5701 ? 584 ? 0.078 26.740 ? ? 9.762 ? ? 584 ? ? ? ? ? 100.000 0.082 ? 0.996 1 13 2.210 2.360 5253 ? 554 ? 0.071 28.250 ? ? 9.482 ? ? 554 ? ? ? ? ? 100.000 0.076 ? 0.997 1 14 2.360 2.550 4920 ? 519 ? 0.068 29.560 ? ? 9.480 ? ? 519 ? ? ? ? ? 100.000 0.071 ? 0.998 1 15 2.550 2.800 4230 ? 453 ? 0.065 30.470 ? ? 9.338 ? ? 453 ? ? ? ? ? 100.000 0.068 ? 0.996 1 16 2.800 3.130 4083 ? 427 ? 0.060 31.260 ? ? 9.562 ? ? 427 ? ? ? ? ? 100.000 0.064 ? 0.998 1 17 3.130 3.610 3635 ? 378 ? 0.056 31.460 ? ? 9.616 ? ? 378 ? ? ? ? ? 100.000 0.060 ? 0.999 1 18 3.610 4.420 2946 ? 322 ? 0.048 31.310 ? ? 9.149 ? ? 322 ? ? ? ? ? 100.000 0.051 ? 0.999 1 19 4.420 6.250 1808 ? 241 ? 0.044 29.330 ? ? 7.502 ? ? 241 ? ? ? ? ? 100.000 0.047 ? 0.999 1 20 6.250 26.111 1190 ? 135 ? 0.054 32.170 ? ? 8.815 ? ? 136 ? ? ? ? ? 99.300 0.058 ? 0.993 # _refine.entry_id 5IX7 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.3980 _refine.ls_d_res_low 26.1110 _refine.pdbx_ls_sigma_F 1.980 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.9500 _refine.ls_number_reflns_obs 11937 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details ? _refine.details 'THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1675 _refine.ls_R_factor_R_work 0.1651 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1886 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 10.0100 _refine.ls_number_reflns_R_free 1195 _refine.ls_number_reflns_R_work 10742 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 25.0900 _refine.solvent_model_param_bsol 44.4990 _refine.solvent_model_param_ksol 0.5420 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.5821 _refine.aniso_B[2][2] 0.5821 _refine.aniso_B[3][3] -1.1643 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.1200 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 0.3000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.0500 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.9069 _refine.B_iso_max 57.200 _refine.B_iso_min 5.280 _refine.pdbx_overall_phase_error 15.7300 _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.3980 _refine_hist.d_res_low 26.1110 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 88 _refine_hist.number_atoms_total 337 _refine_hist.pdbx_number_residues_total 12 _refine_hist.pdbx_B_iso_mean_ligand 16.46 _refine_hist.pdbx_B_iso_mean_solvent 33.59 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 241 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' f_bond_d 269 0.019 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 411 1.310 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 46 0.088 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 12 0.015 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 125 33.488 ? ? ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.R_factor_obs 1.3976 1.4535 9 100.0000 1169 . 0.1939 0.2784 . 166 0.0000 1335 . 'X-RAY DIFFRACTION' . 1.4535 1.5197 9 100.0000 1177 . 0.1873 0.2248 . 140 0.0000 1317 . 'X-RAY DIFFRACTION' . 1.5197 1.5998 9 100.0000 1203 . 0.1997 0.2294 . 126 0.0000 1329 . 'X-RAY DIFFRACTION' . 1.5998 1.7000 9 100.0000 1220 . 0.1761 0.2356 . 114 0.0000 1334 . 'X-RAY DIFFRACTION' . 1.7000 1.8312 9 100.0000 1187 . 0.1648 0.2046 . 106 0.0000 1293 . 'X-RAY DIFFRACTION' . 1.8312 2.0154 9 100.0000 1236 . 0.1741 0.2409 . 127 0.0000 1363 . 'X-RAY DIFFRACTION' . 2.0154 2.3069 9 100.0000 1192 . 0.1524 0.1768 . 124 0.0000 1316 . 'X-RAY DIFFRACTION' . 2.3069 2.9059 9 100.0000 1156 . 0.1361 0.1610 . 167 0.0000 1323 . 'X-RAY DIFFRACTION' . 2.9059 26.1152 9 100.0000 1202 . 0.1690 0.1532 . 125 0.0000 1327 . 'X-RAY DIFFRACTION' . # _struct.entry_id 5IX7 _struct.title 'Crystal structure of metallo-DNA nanowire with infinite one-dimensional silver array' _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 5IX7 _struct_keywords.text 'DNA, nanowire, X-ray analysis, metallo-base pairs, silver' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 3 ? I N N 3 ? J N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5IX7 _struct_ref.pdbx_db_accession 5IX7 _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 5IX7 _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5IX7 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _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 12 # _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)' 5080 ? 1 MORE -86 ? 1 'SSA (A^2)' 3570 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J # 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' 12_555 x,x-y,-z+1/6 0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 19.7366666667 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DT 5 "O3'" ? ? ? 1_555 A CBR 6 P ? ? A DT 5 A CBR 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale both ? A CBR 6 "O3'" ? ? ? 1_555 A DG 7 P ? ? A CBR 6 A DG 7 1_555 ? ? ? ? ? ? ? 1.604 ? ? metalc1 metalc ? ? A DG 1 N7 ? ? ? 1_555 G AG . AG ? ? A DG 1 A AG 106 1_555 ? ? ? ? ? ? ? 2.258 ? ? metalc2 metalc ? ? A DG 1 N7 ? ? ? 1_555 G AG . AG ? ? A DG 1 A AG 106 12_565 ? ? ? ? ? ? ? 2.258 ? ? metalc3 metalc ? ? A DG 2 N1 ? ? ? 1_555 F AG . AG ? ? A DG 2 A AG 105 1_555 ? ? ? ? ? ? ? 2.247 ? ? metalc4 metalc ? ? A DC 4 N3 ? ? ? 1_555 E AG . AG ? ? A DC 4 A AG 104 1_555 ? ? ? ? ? ? ? 2.357 ? ? metalc5 metalc ? ? A DC 4 O2 ? ? ? 1_555 I K . K ? ? A DC 4 A K 108 1_555 ? ? ? ? ? ? ? 2.962 ? ? metalc6 metalc ? ? A DT 5 N3 ? ? ? 1_555 D AG . AG ? ? A DT 5 A AG 103 1_555 ? ? ? ? ? ? ? 2.205 ? ? metalc7 metalc ? ? A DT 5 O2 ? ? ? 1_555 I K . K ? ? A DT 5 A K 108 1_555 ? ? ? ? ? ? ? 2.780 ? ? metalc8 metalc ? ? A CBR 6 N3 ? ? ? 1_555 C AG . AG ? ? A CBR 6 A AG 102 1_555 ? ? ? ? ? ? ? 2.177 ? ? metalc9 metalc ? ? A CBR 6 O2 ? ? ? 1_555 H K . K ? ? A CBR 6 A K 107 1_555 ? ? ? ? ? ? ? 2.611 ? ? metalc10 metalc ? ? A DG 7 N7 ? ? ? 1_555 B AG . AG ? ? A DG 7 A AG 101 1_555 ? ? ? ? ? ? ? 2.322 ? ? metalc11 metalc ? ? A DG 7 N7 ? ? ? 1_555 B AG . AG ? ? A DG 7 A AG 101 12_555 ? ? ? ? ? ? ? 2.323 ? ? metalc12 metalc ? ? A DC 9 N3 ? ? ? 1_555 C AG . AG ? ? A DC 9 A AG 102 12_555 ? ? ? ? ? ? ? 2.268 ? ? metalc13 metalc ? ? A DC 9 O2 ? ? ? 1_555 H K . K ? ? A DC 9 A K 107 12_555 ? ? ? ? ? ? ? 2.729 ? ? metalc14 metalc ? ? A DT 10 N3 ? ? ? 1_555 D AG . AG ? ? A DT 10 A AG 103 12_555 ? ? ? ? ? ? ? 2.196 ? ? metalc15 metalc ? ? A DT 10 "O4'" ? ? ? 1_555 H K . K ? ? A DT 10 A K 107 12_555 ? ? ? ? ? ? ? 2.873 ? ? metalc16 metalc ? ? A DT 10 O2 ? ? ? 1_555 H K . K ? ? A DT 10 A K 107 12_555 ? ? ? ? ? ? ? 2.865 ? ? metalc17 metalc ? ? A DC 11 N3 ? ? ? 1_555 E AG . AG ? ? A DC 11 A AG 104 12_555 ? ? ? ? ? ? ? 2.353 ? ? metalc18 metalc ? ? A DC 11 O2 ? ? ? 1_555 I K . K ? ? A DC 11 A K 108 12_555 ? ? ? ? ? ? ? 2.715 ? ? metalc19 metalc ? ? A DC 12 N3 ? ? ? 1_555 F AG . AG ? ? A DC 12 A AG 105 12_555 ? ? ? ? ? ? ? 2.325 ? ? metalc20 metalc ? ? H K . K ? ? ? 1_555 J HOH . O ? ? A K 107 A HOH 229 8_565 ? ? ? ? ? ? ? 2.794 ? ? metalc21 metalc ? ? H K . K ? ? ? 1_555 J HOH . O ? ? A K 107 A HOH 245 1_555 ? ? ? ? ? ? ? 2.677 ? ? metalc22 metalc ? ? I K . K ? ? ? 1_555 J HOH . O ? ? A K 108 A HOH 251 1_555 ? ? ? ? ? ? ? 2.606 ? ? hydrog1 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 12 N4 ? ? A DG 1 A DC 12 12_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 11 N4 ? ? A DG 2 A DC 11 12_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog3 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 12 O2 ? ? A DG 2 A DC 12 12_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog4 hydrog ? ? A DC 4 N4 ? ? ? 1_555 A DT 10 O4 ? ? A DC 4 A DT 10 12_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog5 hydrog ? ? A DT 5 O4 ? ? ? 1_555 A DC 9 N4 ? ? A DT 5 A DC 9 12_555 ? ? ? ? ? ? 'DT-DC MISPAIR' ? ? ? hydrog6 hydrog ? ? A CBR 6 N4 ? ? ? 1_555 A DG 7 O6 ? ? A CBR 6 A DG 7 12_555 ? ? ? ? ? ? 'CBR-DG MISPAIR' ? ? ? hydrog7 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A CBR 6 N4 ? ? A DG 7 A CBR 6 12_555 ? ? ? ? ? ? 'DG-CBR MISPAIR' ? ? ? hydrog8 hydrog ? ? A DC 9 N4 ? ? ? 1_555 A DT 5 O4 ? ? A DC 9 A DT 5 12_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog9 hydrog ? ? A DT 10 O4 ? ? ? 1_555 A DC 4 N4 ? ? A DT 10 A DC 4 12_555 ? ? ? ? ? ? 'DT-DC MISPAIR' ? ? ? hydrog10 hydrog ? ? A DC 11 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 11 A DG 2 12_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog11 hydrog ? ? A DC 12 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 12 A DG 1 12_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog12 hydrog ? ? A DC 12 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 12 A DG 2 12_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? # 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 N7 ? A DG 1 ? A DG 1 ? 1_555 AG ? G AG . ? A AG 106 ? 1_555 N7 ? A DG 1 ? A DG 1 ? 1_555 0.0 ? 2 N1 ? A DG 2 ? A DG 2 ? 1_555 AG ? F AG . ? A AG 105 ? 1_555 N3 ? A DC 12 ? A DC 12 ? 1_555 61.3 ? 3 N3 ? A DC 4 ? A DC 4 ? 1_555 AG ? E AG . ? A AG 104 ? 1_555 N3 ? A DC 11 ? A DC 11 ? 1_555 67.3 ? 4 O2 ? A DC 4 ? A DC 4 ? 1_555 K ? I K . ? A K 108 ? 1_555 O2 ? A DT 5 ? A DT 5 ? 1_555 83.8 ? 5 O2 ? A DC 4 ? A DC 4 ? 1_555 K ? I K . ? A K 108 ? 1_555 O2 ? A DC 11 ? A DC 11 ? 1_555 74.9 ? 6 O2 ? A DT 5 ? A DT 5 ? 1_555 K ? I K . ? A K 108 ? 1_555 O2 ? A DC 11 ? A DC 11 ? 1_555 8.9 ? 7 O2 ? A DC 4 ? A DC 4 ? 1_555 K ? I K . ? A K 108 ? 1_555 O ? J HOH . ? A HOH 251 ? 1_555 100.8 ? 8 O2 ? A DT 5 ? A DT 5 ? 1_555 K ? I K . ? A K 108 ? 1_555 O ? J HOH . ? A HOH 251 ? 1_555 136.3 ? 9 O2 ? A DC 11 ? A DC 11 ? 1_555 K ? I K . ? A K 108 ? 1_555 O ? J HOH . ? A HOH 251 ? 1_555 136.2 ? 10 N3 ? A DT 5 ? A DT 5 ? 1_555 AG ? D AG . ? A AG 103 ? 1_555 N3 ? A DT 10 ? A DT 10 ? 1_555 85.5 ? 11 N3 ? A CBR 6 ? A CBR 6 ? 1_555 AG ? C AG . ? A AG 102 ? 1_555 N3 ? A DC 9 ? A DC 9 ? 1_555 73.2 ? 12 O2 ? A CBR 6 ? A CBR 6 ? 1_555 K ? H K . ? A K 107 ? 1_555 O2 ? A DC 9 ? A DC 9 ? 1_555 89.5 ? 13 O2 ? A CBR 6 ? A CBR 6 ? 1_555 K ? H K . ? A K 107 ? 1_555 "O4'" ? A DT 10 ? A DT 10 ? 1_555 103.4 ? 14 O2 ? A DC 9 ? A DC 9 ? 1_555 K ? H K . ? A K 107 ? 1_555 "O4'" ? A DT 10 ? A DT 10 ? 1_555 13.9 ? 15 O2 ? A CBR 6 ? A CBR 6 ? 1_555 K ? H K . ? A K 107 ? 1_555 O2 ? A DT 10 ? A DT 10 ? 1_555 85.3 ? 16 O2 ? A DC 9 ? A DC 9 ? 1_555 K ? H K . ? A K 107 ? 1_555 O2 ? A DT 10 ? A DT 10 ? 1_555 6.8 ? 17 "O4'" ? A DT 10 ? A DT 10 ? 1_555 K ? H K . ? A K 107 ? 1_555 O2 ? A DT 10 ? A DT 10 ? 1_555 18.6 ? 18 O2 ? A CBR 6 ? A CBR 6 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 229 ? 8_565 93.1 ? 19 O2 ? A DC 9 ? A DC 9 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 229 ? 8_565 142.2 ? 20 "O4'" ? A DT 10 ? A DT 10 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 229 ? 8_565 139.8 ? 21 O2 ? A DT 10 ? A DT 10 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 229 ? 8_565 147.6 ? 22 O2 ? A CBR 6 ? A CBR 6 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 245 ? 1_555 127.8 ? 23 O2 ? A DC 9 ? A DC 9 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 245 ? 1_555 63.0 ? 24 "O4'" ? A DT 10 ? A DT 10 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 245 ? 1_555 54.5 ? 25 O2 ? A DT 10 ? A DT 10 ? 1_555 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 245 ? 1_555 69.7 ? 26 O ? J HOH . ? A HOH 229 ? 8_565 K ? H K . ? A K 107 ? 1_555 O ? J HOH . ? A HOH 245 ? 1_555 86.4 ? 27 N7 ? A DG 7 ? A DG 7 ? 1_555 AG ? B AG . ? A AG 101 ? 1_555 N7 ? A DG 7 ? A DG 7 ? 1_555 0.0 ? # 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 AG 101 ? 6 'binding site for residue AG A 101' AC2 Software A AG 102 ? 7 'binding site for residue AG A 102' AC3 Software A AG 103 ? 6 'binding site for residue AG A 103' AC4 Software A AG 104 ? 6 'binding site for residue AG A 104' AC5 Software A AG 105 ? 7 'binding site for residue AG A 105' AC6 Software A AG 106 ? 8 'binding site for residue AG A 106' AC7 Software A K 107 ? 6 'binding site for residue K A 107' AC8 Software A K 108 ? 5 'binding site for residue K A 108' # 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 DG A 7 ? DG A 7 . ? 1_555 ? 2 AC1 6 DG A 7 ? DG A 7 . ? 12_555 ? 3 AC1 6 DC A 9 ? DC A 9 . ? 1_555 ? 4 AC1 6 DC A 9 ? DC A 9 . ? 12_555 ? 5 AC1 6 AG C . ? AG A 102 . ? 1_555 ? 6 AC1 6 AG C . ? AG A 102 . ? 12_555 ? 7 AC2 7 DT A 5 ? DT A 5 . ? 1_555 ? 8 AC2 7 CBR A 6 ? CBR A 6 . ? 1_555 ? 9 AC2 7 DG A 7 ? DG A 7 . ? 12_555 ? 10 AC2 7 DC A 9 ? DC A 9 . ? 12_555 ? 11 AC2 7 AG B . ? AG A 101 . ? 12_555 ? 12 AC2 7 AG B . ? AG A 101 . ? 1_555 ? 13 AC2 7 AG D . ? AG A 103 . ? 1_555 ? 14 AC3 6 DC A 4 ? DC A 4 . ? 1_555 ? 15 AC3 6 DT A 5 ? DT A 5 . ? 1_555 ? 16 AC3 6 DC A 9 ? DC A 9 . ? 12_555 ? 17 AC3 6 DT A 10 ? DT A 10 . ? 12_555 ? 18 AC3 6 AG C . ? AG A 102 . ? 1_555 ? 19 AC3 6 AG E . ? AG A 104 . ? 1_555 ? 20 AC4 6 DG A 2 ? DG A 2 . ? 1_555 ? 21 AC4 6 DC A 4 ? DC A 4 . ? 1_555 ? 22 AC4 6 DT A 10 ? DT A 10 . ? 12_555 ? 23 AC4 6 DC A 11 ? DC A 11 . ? 12_555 ? 24 AC4 6 AG D . ? AG A 103 . ? 1_555 ? 25 AC4 6 AG F . ? AG A 105 . ? 1_555 ? 26 AC5 7 DG A 1 ? DG A 1 . ? 1_555 ? 27 AC5 7 DG A 2 ? DG A 2 . ? 1_555 ? 28 AC5 7 DC A 11 ? DC A 11 . ? 12_555 ? 29 AC5 7 DC A 12 ? DC A 12 . ? 12_555 ? 30 AC5 7 AG E . ? AG A 104 . ? 1_555 ? 31 AC5 7 AG G . ? AG A 106 . ? 12_565 ? 32 AC5 7 AG G . ? AG A 106 . ? 1_555 ? 33 AC6 8 DG A 1 ? DG A 1 . ? 12_565 ? 34 AC6 8 DG A 1 ? DG A 1 . ? 1_555 ? 35 AC6 8 DG A 2 ? DG A 2 . ? 12_565 ? 36 AC6 8 DG A 2 ? DG A 2 . ? 1_555 ? 37 AC6 8 AG F . ? AG A 105 . ? 12_565 ? 38 AC6 8 AG F . ? AG A 105 . ? 1_555 ? 39 AC6 8 HOH J . ? HOH A 239 . ? 12_565 ? 40 AC6 8 HOH J . ? HOH A 239 . ? 1_555 ? 41 AC7 6 CBR A 6 ? CBR A 6 . ? 1_555 ? 42 AC7 6 DG A 7 ? DG A 7 . ? 1_555 ? 43 AC7 6 DC A 9 ? DC A 9 . ? 12_555 ? 44 AC7 6 DT A 10 ? DT A 10 . ? 12_555 ? 45 AC7 6 HOH J . ? HOH A 229 . ? 8_565 ? 46 AC7 6 HOH J . ? HOH A 245 . ? 1_555 ? 47 AC8 5 DC A 4 ? DC A 4 . ? 1_555 ? 48 AC8 5 DT A 5 ? DT A 5 . ? 1_555 ? 49 AC8 5 DA A 8 ? DA A 8 . ? 8_565 ? 50 AC8 5 DC A 11 ? DC A 11 . ? 12_555 ? 51 AC8 5 HOH J . ? HOH A 251 . ? 1_555 ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A AG 101 ? B AG . 2 1 A AG 106 ? G AG . 3 1 A HOH 203 ? J HOH . 4 1 A HOH 219 ? J HOH . 5 1 A HOH 232 ? J HOH . 6 1 A HOH 237 ? J HOH . 7 1 A HOH 239 ? J HOH . 8 1 A HOH 248 ? J HOH . 9 1 A HOH 256 ? J HOH . 10 1 A HOH 261 ? J HOH . 11 1 A HOH 268 ? J HOH . # 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 272 ? 6.37 . 2 1 O ? A HOH 273 ? 6.40 . 3 1 O ? A HOH 274 ? 6.54 . 4 1 O ? A HOH 275 ? 7.12 . 5 1 O ? A HOH 276 ? 7.21 . 6 1 O ? A HOH 277 ? 7.42 . 7 1 O ? A HOH 278 ? 7.50 . 8 1 O ? A HOH 279 ? 7.62 . 9 1 O ? A HOH 280 ? 8.11 . 10 1 O ? A HOH 281 ? 8.46 . 11 1 O ? A HOH 282 ? 9.25 . 12 1 O ? A HOH 283 ? 10.08 . 13 1 O ? A HOH 284 ? 10.31 . 14 1 O ? A HOH 285 ? 10.55 . 15 1 O ? A HOH 286 ? 10.89 . 16 1 O ? A HOH 287 ? 11.24 . 17 1 O ? A HOH 288 ? 11.34 . # 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 AG AG AG N N 1 CBR BR BR N N 2 CBR P P N N 3 CBR OP1 O N N 4 CBR OP2 O N N 5 CBR "O5'" O N N 6 CBR N1 N N N 7 CBR C6 C N N 8 CBR C2 C N N 9 CBR O2 O N N 10 CBR N3 N N N 11 CBR C4 C N N 12 CBR N4 N N N 13 CBR C5 C N N 14 CBR "C2'" C N N 15 CBR "C5'" C N N 16 CBR "C4'" C N R 17 CBR "O4'" O N N 18 CBR "C1'" C N R 19 CBR "C3'" C N S 20 CBR "O3'" O N N 21 CBR OP3 O N N 22 CBR HOP2 H N N 23 CBR H6 H N N 24 CBR H41 H N N 25 CBR H42 H N N 26 CBR "H2'" H N N 27 CBR "H2''" H N N 28 CBR "H5'" H N N 29 CBR "H5''" H N N 30 CBR "H4'" H N N 31 CBR "H1'" H N N 32 CBR "H3'" H N N 33 CBR "HO3'" H N N 34 CBR HOP3 H N N 35 DA OP3 O N N 36 DA P P N N 37 DA OP1 O N N 38 DA OP2 O N N 39 DA "O5'" O N N 40 DA "C5'" C N N 41 DA "C4'" C N R 42 DA "O4'" O N N 43 DA "C3'" C N S 44 DA "O3'" O N N 45 DA "C2'" C N N 46 DA "C1'" C N R 47 DA N9 N Y N 48 DA C8 C Y N 49 DA N7 N Y N 50 DA C5 C Y N 51 DA C6 C Y N 52 DA N6 N N N 53 DA N1 N Y N 54 DA C2 C Y N 55 DA N3 N Y N 56 DA C4 C Y N 57 DA HOP3 H N N 58 DA HOP2 H N N 59 DA "H5'" H N N 60 DA "H5''" H N N 61 DA "H4'" H N N 62 DA "H3'" H N N 63 DA "HO3'" H N N 64 DA "H2'" H N N 65 DA "H2''" H N N 66 DA "H1'" H N N 67 DA H8 H N N 68 DA H61 H N N 69 DA H62 H N N 70 DA H2 H N N 71 DC OP3 O N N 72 DC P P N N 73 DC OP1 O N N 74 DC OP2 O N N 75 DC "O5'" O N N 76 DC "C5'" C N N 77 DC "C4'" C N R 78 DC "O4'" O N N 79 DC "C3'" C N S 80 DC "O3'" O N N 81 DC "C2'" C N N 82 DC "C1'" C N R 83 DC N1 N N N 84 DC C2 C N N 85 DC O2 O N N 86 DC N3 N N N 87 DC C4 C N N 88 DC N4 N N N 89 DC C5 C N N 90 DC C6 C N N 91 DC HOP3 H N N 92 DC HOP2 H N N 93 DC "H5'" H N N 94 DC "H5''" H N N 95 DC "H4'" H N N 96 DC "H3'" H N N 97 DC "HO3'" H N N 98 DC "H2'" H N N 99 DC "H2''" H N N 100 DC "H1'" H N N 101 DC H41 H N N 102 DC H42 H N N 103 DC H5 H N N 104 DC H6 H N N 105 DG OP3 O N N 106 DG P P N N 107 DG OP1 O N N 108 DG OP2 O N N 109 DG "O5'" O N N 110 DG "C5'" C N N 111 DG "C4'" C N R 112 DG "O4'" O N N 113 DG "C3'" C N S 114 DG "O3'" O N N 115 DG "C2'" C N N 116 DG "C1'" C N R 117 DG N9 N Y N 118 DG C8 C Y N 119 DG N7 N Y N 120 DG C5 C Y N 121 DG C6 C N N 122 DG O6 O N N 123 DG N1 N N N 124 DG C2 C N N 125 DG N2 N N N 126 DG N3 N N N 127 DG C4 C Y N 128 DG HOP3 H N N 129 DG HOP2 H N N 130 DG "H5'" H N N 131 DG "H5''" H N N 132 DG "H4'" H N N 133 DG "H3'" H N N 134 DG "HO3'" H N N 135 DG "H2'" H N N 136 DG "H2''" H N N 137 DG "H1'" H N N 138 DG H8 H N N 139 DG H1 H N N 140 DG H21 H N N 141 DG H22 H N N 142 DT OP3 O N N 143 DT P P N N 144 DT OP1 O N N 145 DT OP2 O N N 146 DT "O5'" O N N 147 DT "C5'" C N N 148 DT "C4'" C N R 149 DT "O4'" O N N 150 DT "C3'" C N S 151 DT "O3'" O N N 152 DT "C2'" C N N 153 DT "C1'" C N R 154 DT N1 N N N 155 DT C2 C N N 156 DT O2 O N N 157 DT N3 N N N 158 DT C4 C N N 159 DT O4 O N N 160 DT C5 C N N 161 DT C7 C N N 162 DT C6 C N N 163 DT HOP3 H N N 164 DT HOP2 H N N 165 DT "H5'" H N N 166 DT "H5''" H N N 167 DT "H4'" H N N 168 DT "H3'" H N N 169 DT "HO3'" H N N 170 DT "H2'" H N N 171 DT "H2''" H N N 172 DT "H1'" H N N 173 DT H3 H N N 174 DT H71 H N N 175 DT H72 H N N 176 DT H73 H N N 177 DT H6 H N N 178 HOH O O N N 179 HOH H1 H N N 180 HOH H2 H N N 181 K K K N N 182 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DA OP3 P sing N N 36 DA OP3 HOP3 sing N N 37 DA P OP1 doub N N 38 DA P OP2 sing N N 39 DA P "O5'" sing N N 40 DA OP2 HOP2 sing N N 41 DA "O5'" "C5'" sing N N 42 DA "C5'" "C4'" sing N N 43 DA "C5'" "H5'" sing N N 44 DA "C5'" "H5''" sing N N 45 DA "C4'" "O4'" sing N N 46 DA "C4'" "C3'" sing N N 47 DA "C4'" "H4'" sing N N 48 DA "O4'" "C1'" sing N N 49 DA "C3'" "O3'" sing N N 50 DA "C3'" "C2'" sing N N 51 DA "C3'" "H3'" sing N N 52 DA "O3'" "HO3'" sing N N 53 DA "C2'" "C1'" sing N N 54 DA "C2'" "H2'" sing N N 55 DA "C2'" "H2''" sing N N 56 DA "C1'" N9 sing N N 57 DA "C1'" "H1'" sing N N 58 DA N9 C8 sing Y N 59 DA N9 C4 sing Y N 60 DA C8 N7 doub Y N 61 DA C8 H8 sing N N 62 DA N7 C5 sing Y N 63 DA C5 C6 sing Y N 64 DA C5 C4 doub Y N 65 DA C6 N6 sing N N 66 DA C6 N1 doub Y N 67 DA N6 H61 sing N N 68 DA N6 H62 sing N N 69 DA N1 C2 sing Y N 70 DA C2 N3 doub Y N 71 DA C2 H2 sing N N 72 DA N3 C4 sing Y N 73 DC OP3 P sing N N 74 DC OP3 HOP3 sing N N 75 DC P OP1 doub N N 76 DC P OP2 sing N N 77 DC P "O5'" sing N N 78 DC OP2 HOP2 sing N N 79 DC "O5'" "C5'" sing N N 80 DC "C5'" "C4'" sing N N 81 DC "C5'" "H5'" sing N N 82 DC "C5'" "H5''" sing N N 83 DC "C4'" "O4'" sing N N 84 DC "C4'" "C3'" sing N N 85 DC "C4'" "H4'" sing N N 86 DC "O4'" "C1'" sing N N 87 DC "C3'" "O3'" sing N N 88 DC "C3'" "C2'" sing N N 89 DC "C3'" "H3'" sing N N 90 DC "O3'" "HO3'" sing N N 91 DC "C2'" "C1'" sing N N 92 DC "C2'" "H2'" sing N N 93 DC "C2'" "H2''" sing N N 94 DC "C1'" N1 sing N N 95 DC "C1'" "H1'" sing N N 96 DC N1 C2 sing N N 97 DC N1 C6 sing N N 98 DC C2 O2 doub N N 99 DC C2 N3 sing N N 100 DC N3 C4 doub N N 101 DC C4 N4 sing N N 102 DC C4 C5 sing N N 103 DC N4 H41 sing N N 104 DC N4 H42 sing N N 105 DC C5 C6 doub N N 106 DC C5 H5 sing N N 107 DC C6 H6 sing N N 108 DG OP3 P sing N N 109 DG OP3 HOP3 sing N N 110 DG P OP1 doub N N 111 DG P OP2 sing N N 112 DG P "O5'" sing N N 113 DG OP2 HOP2 sing N N 114 DG "O5'" "C5'" sing N N 115 DG "C5'" "C4'" sing N N 116 DG "C5'" "H5'" sing N N 117 DG "C5'" "H5''" sing N N 118 DG "C4'" "O4'" sing N N 119 DG "C4'" "C3'" sing N N 120 DG "C4'" "H4'" sing N N 121 DG "O4'" "C1'" sing N N 122 DG "C3'" "O3'" sing N N 123 DG "C3'" "C2'" sing N N 124 DG "C3'" "H3'" sing N N 125 DG "O3'" "HO3'" sing N N 126 DG "C2'" "C1'" sing N N 127 DG "C2'" "H2'" sing N N 128 DG "C2'" "H2''" sing N N 129 DG "C1'" N9 sing N N 130 DG "C1'" "H1'" sing N N 131 DG N9 C8 sing Y N 132 DG N9 C4 sing Y N 133 DG C8 N7 doub Y N 134 DG C8 H8 sing N N 135 DG N7 C5 sing Y N 136 DG C5 C6 sing N N 137 DG C5 C4 doub Y N 138 DG C6 O6 doub N N 139 DG C6 N1 sing N N 140 DG N1 C2 sing N N 141 DG N1 H1 sing N N 142 DG C2 N2 sing N N 143 DG C2 N3 doub N N 144 DG N2 H21 sing N N 145 DG N2 H22 sing N N 146 DG N3 C4 sing N N 147 DT OP3 P sing N N 148 DT OP3 HOP3 sing N N 149 DT P OP1 doub N N 150 DT P OP2 sing N N 151 DT P "O5'" sing N N 152 DT OP2 HOP2 sing N N 153 DT "O5'" "C5'" sing N N 154 DT "C5'" "C4'" sing N N 155 DT "C5'" "H5'" sing N N 156 DT "C5'" "H5''" sing N N 157 DT "C4'" "O4'" sing N N 158 DT "C4'" "C3'" sing N N 159 DT "C4'" "H4'" sing N N 160 DT "O4'" "C1'" sing N N 161 DT "C3'" "O3'" sing N N 162 DT "C3'" "C2'" sing N N 163 DT "C3'" "H3'" sing N N 164 DT "O3'" "HO3'" sing N N 165 DT "C2'" "C1'" sing N N 166 DT "C2'" "H2'" sing N N 167 DT "C2'" "H2''" sing N N 168 DT "C1'" N1 sing N N 169 DT "C1'" "H1'" sing N N 170 DT N1 C2 sing N N 171 DT N1 C6 sing N N 172 DT C2 O2 doub N N 173 DT C2 N3 sing N N 174 DT N3 C4 sing N N 175 DT N3 H3 sing N N 176 DT C4 O4 doub N N 177 DT C4 C5 sing N N 178 DT C5 C7 sing N N 179 DT C5 C6 doub N N 180 DT C7 H71 sing N N 181 DT C7 H72 sing N N 182 DT C7 H73 sing N N 183 DT C6 H6 sing N N 184 HOH O H1 sing N N 185 HOH O H2 sing N N 186 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5IX7 'double helix' 5IX7 'bulge loop' # 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 DG 2 1_555 A DC 12 12_555 -1.268 1.601 1.159 6.375 -29.041 24.572 1 A_DG2:DC12_A A 2 ? A 12 ? ? ? 1 A DC 4 1_555 A DT 10 12_555 0.249 -0.127 -1.773 -4.133 -52.087 -19.544 2 A_DC4:DT10_A A 4 ? A 10 ? ? ? 1 A DT 5 1_555 A DC 9 12_555 -0.071 -0.502 -2.412 10.875 -52.404 -13.960 3 A_DT5:DC9_A A 5 ? A 9 ? ? ? 1 A CBR 6 1_555 A DG 7 12_555 0.108 3.434 -0.699 -34.057 -21.275 -109.888 4 A_CBR6:DG7_A A 6 ? A 7 ? ? ? 1 A DG 7 1_555 A CBR 6 12_555 -0.108 -3.434 0.699 34.057 21.275 109.888 5 A_DG7:CBR6_A A 7 ? A 6 ? ? ? 1 A DC 9 1_555 A DT 5 12_555 0.071 -0.502 -2.412 -10.875 -52.404 -13.960 6 A_DC9:DT5_A A 9 ? A 5 ? ? ? 1 A DT 10 1_555 A DC 4 12_555 -0.249 -0.127 -1.773 4.133 -52.087 -19.544 7 A_DT10:DC4_A A 10 ? A 4 ? ? ? 1 A DC 12 1_555 A DG 2 12_555 1.268 1.601 1.159 -6.375 -29.041 24.572 8 A_DC12:DG2_A A 12 ? A 2 ? ? ? # 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 DG 2 1_555 A DC 12 12_555 A DC 4 1_555 A DT 10 12_555 0.082 0.177 4.880 -10.312 10.225 54.377 -0.686 -0.969 4.755 10.971 11.064 56.140 1 AA_DG2DC4:DT10DC12_AA A 2 ? A 12 ? A 4 ? A 10 ? 1 A DC 4 1_555 A DT 10 12_555 A DT 5 1_555 A DC 9 12_555 -0.014 0.094 2.443 5.453 3.441 38.379 -0.172 0.516 2.417 5.189 -8.224 38.897 2 AA_DC4DT5:DC9DT10_AA A 4 ? A 10 ? A 5 ? A 9 ? 1 A DT 5 1_555 A DC 9 12_555 A CBR 6 1_555 A DG 7 12_555 1.303 -1.157 2.805 0.574 5.668 89.170 -0.922 -0.917 2.750 4.034 -0.408 89.314 3 AA_DT5CBR6:DG7DC9_AA A 5 ? A 9 ? A 6 ? A 7 ? 1 A CBR 6 1_555 A DG 7 12_555 A DG 7 1_555 A CBR 6 12_555 1.204 -4.979 0.000 -147.744 89.859 180.000 -2.489 -0.602 0.000 44.929 73.872 180.000 4 AA_CBR6DG7:CBR6DG7_AA A 6 ? A 7 ? A 7 ? A 6 ? 1 A DG 7 1_555 A CBR 6 12_555 A DC 9 1_555 A DT 5 12_555 -1.243 -2.714 -1.413 124.140 -122.355 168.440 -1.405 0.573 -1.303 -61.188 -62.080 179.426 5 AA_DG7DC9:DT5CBR6_AA A 7 ? A 6 ? A 9 ? A 5 ? 1 A DC 9 1_555 A DT 5 12_555 A DT 10 1_555 A DC 4 12_555 0.014 0.094 2.443 -5.453 3.441 38.379 -0.172 -0.516 2.417 5.189 8.224 38.897 6 AA_DC9DT10:DC4DT5_AA A 9 ? A 5 ? A 10 ? A 4 ? 1 A DT 10 1_555 A DC 4 12_555 A DC 12 1_555 A DG 2 12_555 -0.082 0.177 4.880 10.312 10.225 54.377 -0.686 0.969 4.755 10.971 -11.064 56.140 7 AA_DT10DC12:DG2DC4_AA A 10 ? A 4 ? A 12 ? A 2 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal MEXT Japan 24245037 1 MEXT Japan S1201015 2 'Murata Science Foundation' Japan ? 3 # _atom_sites.entry_id 5IX7 _atom_sites.fract_transf_matrix[1][1] 0.033167 _atom_sites.fract_transf_matrix[1][2] 0.019149 _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] 0.038299 _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] 0.008445 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol AG B BR C H K N O P # loop_