data_2OJ0 # _entry.id 2OJ0 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2OJ0 pdb_00002oj0 10.2210/pdb2oj0/pdb NDB AR0076 ? ? RCSB RCSB041195 ? ? WWPDB D_1000041195 ? ? # 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 2007-12-25 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-04-18 4 'Structure model' 1 3 2023-12-27 # _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' 'Version format compliance' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.value' 23 4 'Structure model' '_struct_conn.pdbx_dist_value' 24 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 25 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 26 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 27 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 31 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 32 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 33 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 34 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 38 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 39 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 40 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2OJ0 _pdbx_database_status.recvd_initial_deposition_date 2007-01-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2OIY 'HIV-1 subtype B DIS RNA duplex (native)' unspecified PDB 2OIJ 'HIV-1 subtype B DIS RNA duplex (AuCl3 soaked)' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ennifar, E.' 1 'Walter, P.' 2 'Dumas, P.' 3 # _citation.id primary _citation.title 'Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 38 _citation.page_first 5807 _citation.page_last 5816 _citation.year 2010 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20460458 _citation.pdbx_database_id_DOI 10.1093/nar/gkq344 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ennifar, E.' 1 ? primary 'Walter, P.' 2 ? primary 'Dumas, P.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3'" 7417.488 2 ? ? ? 'HIV-1 subtype-B DIS RNA, dimerization initiation site' 2 non-polymer syn 'POTASSIUM ION' 39.098 5 ? ? ? ? 3 non-polymer syn 'MANGANESE (II) ION' 54.938 3 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 3 ? ? ? ? 5 water nat water 18.015 149 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CUUGCUGAAGCGCGCACGGCAAG _entity_poly.pdbx_seq_one_letter_code_can CUUGCUGAAGCGCGCACGGCAAG _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 'POTASSIUM ION' K 3 'MANGANESE (II) ION' MN 4 'SODIUM ION' NA 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 U n 1 4 G n 1 5 C n 1 6 U n 1 7 G n 1 8 A n 1 9 A n 1 10 G n 1 11 C n 1 12 G n 1 13 C n 1 14 G n 1 15 C n 1 16 A n 1 17 C n 1 18 G n 1 19 G n 1 20 C n 1 21 A n 1 22 A n 1 23 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'HIV-1 GENOMIC RNA LAI ISOLATE (HIV-1 SUBTYPE B)' # 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C C A . n A 1 2 U 2 2 2 U U A . n A 1 3 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 C 5 5 5 C C A . n A 1 6 U 6 6 6 U U A . n A 1 7 G 7 7 7 G G A . n A 1 8 A 8 8 8 A A A . n A 1 9 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . n A 1 13 C 13 13 13 C C A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 A 16 16 16 A A A . n A 1 17 C 17 17 17 C C A . n A 1 18 G 18 18 18 G G A . n A 1 19 G 19 19 19 G G A . n A 1 20 C 20 20 20 C C A . n A 1 21 A 21 21 21 A A A . n A 1 22 A 22 22 22 A A A . n A 1 23 G 23 23 23 G G A . n B 1 1 C 1 1 1 C C B . n B 1 2 U 2 2 2 U U B . n B 1 3 U 3 3 3 U U B . n B 1 4 G 4 4 4 G G B . n B 1 5 C 5 5 5 C C B . n B 1 6 U 6 6 6 U U B . n B 1 7 G 7 7 7 G G B . n B 1 8 A 8 8 8 A A B . n B 1 9 A 9 9 9 A A B . n B 1 10 G 10 10 10 G G B . n B 1 11 C 11 11 11 C C B . n B 1 12 G 12 12 12 G G B . n B 1 13 C 13 13 13 C C B . n B 1 14 G 14 14 14 G G B . n B 1 15 C 15 15 15 C C B . n B 1 16 A 16 16 16 A A B . n B 1 17 C 17 17 17 C C B . n B 1 18 G 18 18 18 G G B . n B 1 19 G 19 19 19 G G B . n B 1 20 C 20 20 20 C C B . n B 1 21 A 21 21 21 A A B . n B 1 22 A 22 22 22 A A B . n B 1 23 G 23 23 23 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 K 1 201 201 K K A . D 2 K 1 203 203 K K A . E 3 MN 1 205 205 MN MN A . F 4 NA 1 262 262 NA NA A . G 4 NA 1 315 315 NA NA A . H 2 K 1 202 202 K K B . I 3 MN 1 204 204 MN MN B . J 3 MN 1 206 206 MN MN B . K 2 K 1 207 207 K K B . L 2 K 1 208 208 K K B . M 4 NA 1 209 209 NA NA B . N 5 HOH 1 316 3 HOH HOH A . N 5 HOH 2 317 7 HOH HOH A . N 5 HOH 3 318 10 HOH HOH A . N 5 HOH 4 319 11 HOH HOH A . N 5 HOH 5 320 12 HOH HOH A . N 5 HOH 6 321 14 HOH HOH A . N 5 HOH 7 322 15 HOH HOH A . N 5 HOH 8 323 16 HOH HOH A . N 5 HOH 9 324 17 HOH HOH A . N 5 HOH 10 325 19 HOH HOH A . N 5 HOH 11 326 21 HOH HOH A . N 5 HOH 12 327 22 HOH HOH A . N 5 HOH 13 328 23 HOH HOH A . N 5 HOH 14 329 24 HOH HOH A . N 5 HOH 15 330 25 HOH HOH A . N 5 HOH 16 331 26 HOH HOH A . N 5 HOH 17 332 27 HOH HOH A . N 5 HOH 18 333 28 HOH HOH A . N 5 HOH 19 334 29 HOH HOH A . N 5 HOH 20 335 32 HOH HOH A . N 5 HOH 21 336 34 HOH HOH A . N 5 HOH 22 337 35 HOH HOH A . N 5 HOH 23 338 36 HOH HOH A . N 5 HOH 24 339 37 HOH HOH A . N 5 HOH 25 340 40 HOH HOH A . N 5 HOH 26 341 41 HOH HOH A . N 5 HOH 27 342 42 HOH HOH A . N 5 HOH 28 343 44 HOH HOH A . N 5 HOH 29 344 45 HOH HOH A . N 5 HOH 30 345 46 HOH HOH A . N 5 HOH 31 346 48 HOH HOH A . N 5 HOH 32 347 55 HOH HOH A . N 5 HOH 33 348 60 HOH HOH A . N 5 HOH 34 349 66 HOH HOH A . N 5 HOH 35 350 67 HOH HOH A . N 5 HOH 36 351 70 HOH HOH A . N 5 HOH 37 352 71 HOH HOH A . N 5 HOH 38 353 72 HOH HOH A . N 5 HOH 39 354 73 HOH HOH A . N 5 HOH 40 355 74 HOH HOH A . N 5 HOH 41 356 75 HOH HOH A . N 5 HOH 42 357 76 HOH HOH A . N 5 HOH 43 358 77 HOH HOH A . N 5 HOH 44 359 79 HOH HOH A . N 5 HOH 45 360 80 HOH HOH A . N 5 HOH 46 361 82 HOH HOH A . N 5 HOH 47 362 84 HOH HOH A . N 5 HOH 48 363 85 HOH HOH A . N 5 HOH 49 364 89 HOH HOH A . N 5 HOH 50 365 90 HOH HOH A . N 5 HOH 51 366 91 HOH HOH A . N 5 HOH 52 367 92 HOH HOH A . N 5 HOH 53 368 93 HOH HOH A . N 5 HOH 54 369 95 HOH HOH A . N 5 HOH 55 370 97 HOH HOH A . N 5 HOH 56 371 98 HOH HOH A . N 5 HOH 57 372 99 HOH HOH A . N 5 HOH 58 373 107 HOH HOH A . N 5 HOH 59 374 108 HOH HOH A . N 5 HOH 60 375 113 HOH HOH A . N 5 HOH 61 376 117 HOH HOH A . N 5 HOH 62 377 118 HOH HOH A . N 5 HOH 63 378 119 HOH HOH A . N 5 HOH 64 379 123 HOH HOH A . N 5 HOH 65 380 124 HOH HOH A . N 5 HOH 66 381 125 HOH HOH A . N 5 HOH 67 382 129 HOH HOH A . N 5 HOH 68 383 131 HOH HOH A . N 5 HOH 69 384 132 HOH HOH A . N 5 HOH 70 385 136 HOH HOH A . N 5 HOH 71 386 138 HOH HOH A . N 5 HOH 72 387 139 HOH HOH A . N 5 HOH 73 388 141 HOH HOH A . N 5 HOH 74 389 142 HOH HOH A . N 5 HOH 75 390 143 HOH HOH A . N 5 HOH 76 391 144 HOH HOH A . N 5 HOH 77 392 147 HOH HOH A . N 5 HOH 78 393 148 HOH HOH A . N 5 HOH 79 394 149 HOH HOH A . N 5 HOH 80 395 150 HOH HOH A . N 5 HOH 81 396 154 HOH HOH A . N 5 HOH 82 397 156 HOH HOH A . O 5 HOH 1 210 4 HOH HOH B . O 5 HOH 2 211 5 HOH HOH B . O 5 HOH 3 212 6 HOH HOH B . O 5 HOH 4 213 8 HOH HOH B . O 5 HOH 5 214 9 HOH HOH B . O 5 HOH 6 215 13 HOH HOH B . O 5 HOH 7 216 18 HOH HOH B . O 5 HOH 8 217 20 HOH HOH B . O 5 HOH 9 218 30 HOH HOH B . O 5 HOH 10 219 31 HOH HOH B . O 5 HOH 11 220 33 HOH HOH B . O 5 HOH 12 221 38 HOH HOH B . O 5 HOH 13 222 39 HOH HOH B . O 5 HOH 14 223 43 HOH HOH B . O 5 HOH 15 224 47 HOH HOH B . O 5 HOH 16 225 49 HOH HOH B . O 5 HOH 17 226 50 HOH HOH B . O 5 HOH 18 227 51 HOH HOH B . O 5 HOH 19 228 52 HOH HOH B . O 5 HOH 20 229 53 HOH HOH B . O 5 HOH 21 230 54 HOH HOH B . O 5 HOH 22 231 56 HOH HOH B . O 5 HOH 23 232 57 HOH HOH B . O 5 HOH 24 233 58 HOH HOH B . O 5 HOH 25 234 59 HOH HOH B . O 5 HOH 26 235 61 HOH HOH B . O 5 HOH 27 236 63 HOH HOH B . O 5 HOH 28 237 64 HOH HOH B . O 5 HOH 29 238 65 HOH HOH B . O 5 HOH 30 239 68 HOH HOH B . O 5 HOH 31 240 69 HOH HOH B . O 5 HOH 32 241 78 HOH HOH B . O 5 HOH 33 242 81 HOH HOH B . O 5 HOH 34 243 83 HOH HOH B . O 5 HOH 35 244 86 HOH HOH B . O 5 HOH 36 245 87 HOH HOH B . O 5 HOH 37 246 88 HOH HOH B . O 5 HOH 38 247 94 HOH HOH B . O 5 HOH 39 248 96 HOH HOH B . O 5 HOH 40 249 100 HOH HOH B . O 5 HOH 41 250 101 HOH HOH B . O 5 HOH 42 251 102 HOH HOH B . O 5 HOH 43 252 103 HOH HOH B . O 5 HOH 44 253 104 HOH HOH B . O 5 HOH 45 254 105 HOH HOH B . O 5 HOH 46 255 106 HOH HOH B . O 5 HOH 47 256 109 HOH HOH B . O 5 HOH 48 257 110 HOH HOH B . O 5 HOH 49 258 111 HOH HOH B . O 5 HOH 50 259 112 HOH HOH B . O 5 HOH 51 260 114 HOH HOH B . O 5 HOH 52 261 120 HOH HOH B . O 5 HOH 53 262 121 HOH HOH B . O 5 HOH 54 263 122 HOH HOH B . O 5 HOH 55 264 126 HOH HOH B . O 5 HOH 56 265 130 HOH HOH B . O 5 HOH 57 266 133 HOH HOH B . O 5 HOH 58 267 134 HOH HOH B . O 5 HOH 59 268 135 HOH HOH B . O 5 HOH 60 269 137 HOH HOH B . O 5 HOH 61 270 140 HOH HOH B . O 5 HOH 62 271 145 HOH HOH B . O 5 HOH 63 272 146 HOH HOH B . O 5 HOH 64 273 151 HOH HOH B . O 5 HOH 65 274 152 HOH HOH B . O 5 HOH 66 275 153 HOH HOH B . O 5 HOH 67 276 155 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHARP phasing . ? 1 CNS refinement 1.0 ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 2OJ0 _cell.length_a 42.538 _cell.length_b 47.834 _cell.length_c 58.681 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2OJ0 _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2OJ0 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.01 _exptl_crystal.density_percent_sol 38.87 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'MPD, POTASSIUM CHLORIDE, MAGNESIUM CHLORIDE, CACODYLATE, SPERMINE, pH 7.00, VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 'POTASSIUM CHLORIDE' ? ? ? 1 3 1 'MAGNESIUM CHLORIDE' ? ? ? 1 4 1 CACODYLATE ? ? ? 1 5 1 SPERMINE ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MPD ? ? ? 1 8 2 'POTASSIUM CHLORIDE' ? ? ? 1 9 2 'MAGNESIUM CHLORIDE' ? ? ? 1 10 2 CACODYLATE ? ? ? 1 11 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2001-06-04 _diffrn_detector.details crystal # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator CRYSTAL _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.409 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM30A' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM30A _diffrn_source.pdbx_wavelength 1.409 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 2OJ0 _reflns.observed_criterion_sigma_I 1.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 2.600 _reflns.number_obs 7223 _reflns.number_all 7226 _reflns.percent_possible_obs 98.4 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.06 _reflns.pdbx_netI_over_sigmaI 21.1 _reflns.B_iso_Wilson_estimate 29.30 _reflns.pdbx_redundancy 3.300 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.60 _reflns_shell.d_res_low 2.69 _reflns_shell.percent_possible_all 92.7 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.083 _reflns_shell.meanI_over_sigI_obs 12.0 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 694 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 2OJ0 _refine.ls_number_reflns_obs 6735 _refine.ls_number_reflns_all 6894 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 7.97 _refine.ls_d_res_high 2.60 _refine.ls_percent_reflns_obs 97.7 _refine.ls_R_factor_obs 0.2 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2 _refine.ls_R_factor_R_free 0.23 _refine.ls_R_factor_R_free_error 0.010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.400 _refine.ls_number_reflns_R_free 565 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 20.40 _refine.aniso_B[1][1] -1.71000 _refine.aniso_B[2][2] 1.26000 _refine.aniso_B[3][3] 0.45000 _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 'FLAT MODEL' _refine.solvent_model_param_ksol 0.38 _refine.solvent_model_param_bsol 25.45 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MIR _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 2OJ0 _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.36 _refine_analyze.Luzzati_sigma_a_free 0.34 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 982 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 149 _refine_hist.number_atoms_total 1142 _refine_hist.d_res_high 2.60 _refine_hist.d_res_low 7.97 # 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 c_bond_d 0.003 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.90 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 8.10 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.40 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.60 _refine_ls_shell.d_res_low 2.76 _refine_ls_shell.number_reflns_R_work 1001 _refine_ls_shell.R_factor_R_work 0.303 _refine_ls_shell.percent_reflns_obs 96.10 _refine_ls_shell.R_factor_R_free 0.31 _refine_ls_shell.R_factor_R_free_error 0.030 _refine_ls_shell.percent_reflns_R_free 9.50 _refine_ls_shell.number_reflns_R_free 105 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 ION.PARAM WATER.TOP 'X-RAY DIFFRACTION' 4 LUC.PARAM ION.TOP 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 2OJ0 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2OJ0 _struct.title 'Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2OJ0 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HIV-1, DIS, RNA, DIMERIZATION, metal ions' # 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 3 ? F N N 4 ? G N N 4 ? H N N 2 ? I N N 3 ? J N N 3 ? K N N 2 ? L N N 2 ? M N N 4 ? N N N 5 ? O N N 5 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2OJ0 _struct_ref.pdbx_db_accession 2OJ0 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 2OJ0 A 1 ? 23 ? 2OJ0 1 ? 23 ? 1 23 2 1 2OJ0 B 1 ? 23 ? 2OJ0 1 ? 23 ? 1 23 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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,I,J,K,L,M,N,O # _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 # _struct_biol.id 1 _struct_biol.details ? # 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 metalc1 metalc ? ? A U 6 O4 ? ? ? 1_555 D K . K ? ? A U 6 A K 203 1_555 ? ? ? ? ? ? ? 2.766 ? ? metalc2 metalc ? ? A G 7 O6 ? ? ? 1_555 D K . K ? ? A G 7 A K 203 1_555 ? ? ? ? ? ? ? 2.724 ? ? metalc3 metalc ? ? A C 13 OP1 ? ? ? 1_555 G NA . NA ? ? A C 13 A NA 315 1_555 ? ? ? ? ? ? ? 2.454 ? ? metalc4 metalc ? ? C K . K ? ? ? 1_555 N HOH . O ? ? A K 201 A HOH 326 1_555 ? ? ? ? ? ? ? 3.362 ? ? metalc5 metalc ? ? D K . K ? ? ? 1_555 B G 18 O6 ? ? A K 203 B G 18 1_555 ? ? ? ? ? ? ? 2.725 ? ? metalc6 metalc ? ? N HOH . O ? ? ? 1_555 H K . K ? ? A HOH 335 B K 202 1_555 ? ? ? ? ? ? ? 3.433 ? ? metalc7 metalc ? ? N HOH . O ? ? ? 1_555 H K . K ? ? A HOH 376 B K 202 1_555 ? ? ? ? ? ? ? 3.399 ? ? metalc8 metalc ? ? B U 3 O4 ? ? ? 1_555 H K . K ? ? B U 3 B K 202 1_555 ? ? ? ? ? ? ? 3.454 ? ? metalc9 metalc ? ? B G 4 "O2'" ? ? ? 1_555 K K . K ? ? B G 4 B K 207 1_555 ? ? ? ? ? ? ? 2.942 ? ? metalc10 metalc ? ? B A 9 OP1 ? ? ? 1_555 I MN . MN ? ? B A 9 B MN 204 1_555 ? ? ? ? ? ? ? 1.977 ? ? metalc11 metalc ? ? B G 10 OP1 ? ? ? 1_555 I MN . MN ? ? B G 10 B MN 204 1_555 ? ? ? ? ? ? ? 2.315 ? ? metalc12 metalc ? ? B G 10 N7 ? ? ? 1_555 I MN . MN ? ? B G 10 B MN 204 1_555 ? ? ? ? ? ? ? 2.362 ? ? metalc13 metalc ? ? B G 10 "O2'" ? ? ? 1_555 L K . K ? ? B G 10 B K 208 1_555 ? ? ? ? ? ? ? 2.693 ? ? metalc14 metalc ? ? B G 10 "O3'" ? ? ? 1_555 L K . K ? ? B G 10 B K 208 1_555 ? ? ? ? ? ? ? 3.199 ? ? metalc15 metalc ? ? B G 14 O6 ? ? ? 1_555 J MN . MN ? ? B G 14 B MN 206 1_555 ? ? ? ? ? ? ? 2.239 ? ? metalc16 metalc ? ? I MN . MN ? ? ? 1_555 O HOH . O ? ? B MN 204 B HOH 240 1_555 ? ? ? ? ? ? ? 2.409 ? ? metalc17 metalc ? ? M NA . NA ? ? ? 1_555 O HOH . O ? ? B NA 209 B HOH 219 1_555 ? ? ? ? ? ? ? 2.654 ? ? metalc18 metalc ? ? M NA . NA ? ? ? 1_555 O HOH . O ? ? B NA 209 B HOH 260 1_555 ? ? ? ? ? ? ? 3.191 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 23 N1 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 23 O6 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 23 N2 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 22 N1 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 22 N6 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 B A 21 N1 ? ? A U 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 B A 21 N6 ? ? A U 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 B G 18 O6 ? ? A U 6 B G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A U 6 O2 ? ? ? 1_555 B G 18 N1 ? ? A U 6 B G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 17 N3 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 17 O2 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 17 N4 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 14 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 14 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 14 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 17 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 17 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 17 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 18 N1 ? ? ? 1_555 B U 6 O2 ? ? A G 18 B U 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog41 hydrog ? ? A G 18 O6 ? ? ? 1_555 B U 6 N3 ? ? A G 18 B U 6 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog42 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A A 21 N1 ? ? ? 1_555 B U 3 N3 ? ? A A 21 B U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 21 N6 ? ? ? 1_555 B U 3 O4 ? ? A A 21 B U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A A 22 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A A 22 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 23 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 23 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 23 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 O4 ? A U 6 ? A U 6 ? 1_555 K ? D K . ? A K 203 ? 1_555 O6 ? A G 7 ? A G 7 ? 1_555 82.3 ? 2 O4 ? A U 6 ? A U 6 ? 1_555 K ? D K . ? A K 203 ? 1_555 O6 ? B G 18 ? B G 18 ? 1_555 75.3 ? 3 O6 ? A G 7 ? A G 7 ? 1_555 K ? D K . ? A K 203 ? 1_555 O6 ? B G 18 ? B G 18 ? 1_555 66.6 ? 4 O ? N HOH . ? A HOH 335 ? 1_555 K ? H K . ? B K 202 ? 1_555 O ? N HOH . ? A HOH 376 ? 1_555 82.8 ? 5 O ? N HOH . ? A HOH 335 ? 1_555 K ? H K . ? B K 202 ? 1_555 O4 ? B U 3 ? B U 3 ? 1_555 144.9 ? 6 O ? N HOH . ? A HOH 376 ? 1_555 K ? H K . ? B K 202 ? 1_555 O4 ? B U 3 ? B U 3 ? 1_555 117.5 ? 7 OP1 ? B A 9 ? B A 9 ? 1_555 MN ? I MN . ? B MN 204 ? 1_555 OP1 ? B G 10 ? B G 10 ? 1_555 89.1 ? 8 OP1 ? B A 9 ? B A 9 ? 1_555 MN ? I MN . ? B MN 204 ? 1_555 N7 ? B G 10 ? B G 10 ? 1_555 160.6 ? 9 OP1 ? B G 10 ? B G 10 ? 1_555 MN ? I MN . ? B MN 204 ? 1_555 N7 ? B G 10 ? B G 10 ? 1_555 98.8 ? 10 OP1 ? B A 9 ? B A 9 ? 1_555 MN ? I MN . ? B MN 204 ? 1_555 O ? O HOH . ? B HOH 240 ? 1_555 83.7 ? 11 OP1 ? B G 10 ? B G 10 ? 1_555 MN ? I MN . ? B MN 204 ? 1_555 O ? O HOH . ? B HOH 240 ? 1_555 85.2 ? 12 N7 ? B G 10 ? B G 10 ? 1_555 MN ? I MN . ? B MN 204 ? 1_555 O ? O HOH . ? B HOH 240 ? 1_555 79.3 ? 13 "O2'" ? B G 10 ? B G 10 ? 1_555 K ? L K . ? B K 208 ? 1_555 "O3'" ? B G 10 ? B G 10 ? 1_555 55.6 ? 14 O ? O HOH . ? B HOH 219 ? 1_555 NA ? M NA . ? B NA 209 ? 1_555 O ? O HOH . ? B HOH 260 ? 1_555 108.6 ? # 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 K 201 ? 1 'BINDING SITE FOR RESIDUE K A 201' AC2 Software B K 202 ? 2 'BINDING SITE FOR RESIDUE K B 202' AC3 Software A K 203 ? 4 'BINDING SITE FOR RESIDUE K A 203' AC4 Software B MN 204 ? 3 'BINDING SITE FOR RESIDUE MN B 204' AC5 Software A MN 205 ? 1 'BINDING SITE FOR RESIDUE MN A 205' AC6 Software B MN 206 ? 3 'BINDING SITE FOR RESIDUE MN B 206' AC7 Software B K 207 ? 4 'BINDING SITE FOR RESIDUE K B 207' AC8 Software B K 208 ? 3 'BINDING SITE FOR RESIDUE K B 208' AC9 Software B NA 209 ? 2 'BINDING SITE FOR RESIDUE NA B 209' BC1 Software A NA 315 ? 5 'BINDING SITE FOR RESIDUE NA A 315' # 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 1 G A 4 ? G A 4 . ? 1_555 ? 2 AC2 2 G A 19 ? G A 19 . ? 1_555 ? 3 AC2 2 U B 3 ? U B 3 . ? 1_555 ? 4 AC3 4 U A 6 ? U A 6 . ? 1_555 ? 5 AC3 4 G A 7 ? G A 7 . ? 1_555 ? 6 AC3 4 C B 17 ? C B 17 . ? 1_555 ? 7 AC3 4 G B 18 ? G B 18 . ? 1_555 ? 8 AC4 3 A B 9 ? A B 9 . ? 1_555 ? 9 AC4 3 G B 10 ? G B 10 . ? 1_555 ? 10 AC4 3 HOH O . ? HOH B 240 . ? 1_555 ? 11 AC5 1 HOH N . ? HOH A 373 . ? 1_555 ? 12 AC6 3 C A 11 ? C A 11 . ? 1_555 ? 13 AC6 3 G B 14 ? G B 14 . ? 1_555 ? 14 AC6 3 HOH O . ? HOH B 244 . ? 1_555 ? 15 AC7 4 G A 4 ? G A 4 . ? 4_473 ? 16 AC7 4 G B 4 ? G B 4 . ? 1_555 ? 17 AC7 4 C B 20 ? C B 20 . ? 4_473 ? 18 AC7 4 A B 21 ? A B 21 . ? 4_473 ? 19 AC8 3 G A 10 ? G A 10 . ? 4_573 ? 20 AC8 3 HOH N . ? HOH A 330 . ? 4_573 ? 21 AC8 3 G B 10 ? G B 10 . ? 1_555 ? 22 AC9 2 C B 11 ? C B 11 . ? 1_555 ? 23 AC9 2 HOH O . ? HOH B 219 . ? 1_555 ? 24 BC1 5 A A 8 ? A A 8 . ? 4_473 ? 25 BC1 5 G A 12 ? G A 12 . ? 1_555 ? 26 BC1 5 C A 13 ? C A 13 . ? 1_555 ? 27 BC1 5 HOH N . ? HOH A 381 . ? 4_473 ? 28 BC1 5 HOH N . ? HOH A 390 . ? 4_473 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 7 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.065 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 K K K N N 114 MN MN MN N N 115 NA NA NA N N 116 U OP3 O N N 117 U P P N N 118 U OP1 O N N 119 U OP2 O N N 120 U "O5'" O N N 121 U "C5'" C N N 122 U "C4'" C N R 123 U "O4'" O N N 124 U "C3'" C N S 125 U "O3'" O N N 126 U "C2'" C N R 127 U "O2'" O N N 128 U "C1'" C N R 129 U N1 N N N 130 U C2 C N N 131 U O2 O N N 132 U N3 N N N 133 U C4 C N N 134 U O4 O N N 135 U C5 C N N 136 U C6 C N N 137 U HOP3 H N N 138 U HOP2 H N N 139 U "H5'" H N N 140 U "H5''" H N N 141 U "H4'" H N N 142 U "H3'" H N N 143 U "HO3'" H N N 144 U "H2'" H N N 145 U "HO2'" H N N 146 U "H1'" H N N 147 U H3 H N N 148 U H5 H N N 149 U H6 H N N 150 # 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 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2OJ0 'double helix' 2OJ0 'a-form double helix' 2OJ0 'mismatched base pair' 2OJ0 'internal 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 C 1 1_555 B G 23 1_555 -0.812 -0.406 0.215 0.077 -16.461 -3.420 1 A_C1:G23_B A 1 ? B 23 ? 19 1 1 A U 2 1_555 B A 22 1_555 0.082 -0.266 0.063 -4.964 -15.615 0.864 2 A_U2:A22_B A 2 ? B 22 ? 20 1 1 A U 3 1_555 B A 21 1_555 -0.146 -0.066 0.186 -0.872 -7.918 1.092 3 A_U3:A21_B A 3 ? B 21 ? 20 1 1 A G 4 1_555 B C 20 1_555 -0.435 -0.144 0.173 1.487 -8.495 3.366 4 A_G4:C20_B A 4 ? B 20 ? 19 1 1 A C 5 1_555 B G 19 1_555 0.665 -0.040 -0.081 0.459 -15.137 -0.364 5 A_C5:G19_B A 5 ? B 19 ? 19 1 1 A U 6 1_555 B G 18 1_555 1.640 -0.412 0.115 5.637 -12.932 0.612 6 A_U6:G18_B A 6 ? B 18 ? 28 1 1 A G 7 1_555 B C 17 1_555 -0.361 -0.248 -0.352 14.324 6.349 2.179 7 A_G7:C17_B A 7 ? B 17 ? 19 1 1 A G 10 1_555 B C 15 1_555 -0.512 -0.210 -0.510 -5.111 -13.115 -3.100 8 A_G10:C15_B A 10 ? B 15 ? 19 1 1 A C 11 1_555 B G 14 1_555 0.418 0.040 -0.428 8.586 -8.658 7.514 9 A_C11:G14_B A 11 ? B 14 ? 19 1 1 A G 12 1_555 B C 13 1_555 -0.521 -0.123 -0.115 -2.308 2.557 -1.373 10 A_G12:C13_B A 12 ? B 13 ? 19 1 1 A C 13 1_555 B G 12 1_555 0.157 0.027 -0.118 1.003 -4.811 5.130 11 A_C13:G12_B A 13 ? B 12 ? 19 1 1 A G 14 1_555 B C 11 1_555 -0.120 -0.239 -0.569 -7.655 -3.736 1.278 12 A_G14:C11_B A 14 ? B 11 ? 19 1 1 A C 15 1_555 B G 10 1_555 0.496 -0.240 -0.417 5.335 -2.951 3.691 13 A_C15:G10_B A 15 ? B 10 ? 19 1 1 A C 17 1_555 B G 7 1_555 0.821 -0.330 -0.199 -9.081 4.779 1.581 14 A_C17:G7_B A 17 ? B 7 ? 19 1 1 A G 18 1_555 B U 6 1_555 -2.148 -0.552 -0.133 1.318 -7.385 1.797 15 A_G18:U6_B A 18 ? B 6 ? 28 1 1 A G 19 1_555 B C 5 1_555 -0.609 -0.197 -0.143 2.086 -16.337 4.337 16 A_G19:C5_B A 19 ? B 5 ? 19 1 1 A C 20 1_555 B G 4 1_555 0.290 -0.194 0.112 2.417 -11.092 -1.806 17 A_C20:G4_B A 20 ? B 4 ? 19 1 1 A A 21 1_555 B U 3 1_555 0.254 0.002 0.342 -0.999 -12.983 7.607 18 A_A21:U3_B A 21 ? B 3 ? 20 1 1 A A 22 1_555 B U 2 1_555 0.864 -0.305 0.116 -0.337 -13.841 -3.546 19 A_A22:U2_B A 22 ? B 2 ? 20 1 1 A G 23 1_555 B C 1 1_555 -0.022 -0.303 -0.369 -13.622 -19.634 -8.491 20 A_G23:C1_B A 23 ? 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 C 1 1_555 B G 23 1_555 A U 2 1_555 B A 22 1_555 -0.274 -1.400 3.284 -0.857 10.515 39.518 -3.107 0.303 2.841 15.225 1.241 40.848 1 AA_C1U2:A22G23_BB A 1 ? B 23 ? A 2 ? B 22 ? 1 A U 2 1_555 B A 22 1_555 A U 3 1_555 B A 21 1_555 0.176 -1.134 3.134 -0.793 8.501 32.030 -3.299 -0.430 2.746 15.074 1.406 33.119 2 AA_U2U3:A21A22_BB A 2 ? B 22 ? A 3 ? B 21 ? 1 A U 3 1_555 B A 21 1_555 A G 4 1_555 B C 20 1_555 0.577 -1.554 2.971 1.643 10.684 29.610 -4.528 -0.807 2.312 20.082 -3.089 31.480 3 AA_U3G4:C20A21_BB A 3 ? B 21 ? A 4 ? B 20 ? 1 A G 4 1_555 B C 20 1_555 A C 5 1_555 B G 19 1_555 -0.587 -1.380 3.247 0.262 12.175 36.333 -3.526 0.926 2.661 18.883 -0.406 38.254 4 AA_G4C5:G19C20_BB A 4 ? B 20 ? A 5 ? B 19 ? 1 A C 5 1_555 B G 19 1_555 A U 6 1_555 B G 18 1_555 0.568 -1.520 3.150 1.004 6.983 36.339 -3.262 -0.770 2.833 11.069 -1.592 36.995 5 AA_C5U6:G18G19_BB A 5 ? B 19 ? A 6 ? B 18 ? 1 A U 6 1_555 B G 18 1_555 A G 7 1_555 B C 17 1_555 0.208 -2.107 2.993 3.705 14.958 17.782 -8.675 0.357 0.974 39.990 -9.906 23.489 6 AA_U6G7:C17G18_BB A 6 ? B 18 ? A 7 ? B 17 ? 1 A G 7 1_555 B C 17 1_555 A G 10 1_555 B C 15 1_555 -1.821 -1.999 6.848 -11.639 13.006 68.680 -2.683 0.722 6.626 11.343 10.151 70.599 7 AA_G7G10:C15C17_BB A 7 ? B 17 ? A 10 ? B 15 ? 1 A G 10 1_555 B C 15 1_555 A C 11 1_555 B G 14 1_555 1.259 -0.979 2.796 0.890 7.053 37.407 -2.247 -1.837 2.604 10.877 -1.373 38.053 8 AA_G10C11:G14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A C 11 1_555 B G 14 1_555 A G 12 1_555 B C 13 1_555 -1.400 -2.577 3.598 -6.027 9.579 23.344 -8.409 1.448 2.629 22.087 13.896 25.908 9 AA_C11G12:C13G14_BB A 11 ? B 14 ? A 12 ? B 13 ? 1 A G 12 1_555 B C 13 1_555 A C 13 1_555 B G 12 1_555 1.122 -2.152 3.256 2.397 -0.083 31.808 -3.902 -1.603 3.335 -0.152 -4.366 31.896 10 AA_G12C13:G12C13_BB A 12 ? B 13 ? A 13 ? B 12 ? 1 A C 13 1_555 B G 12 1_555 A G 14 1_555 B C 11 1_555 -0.709 -1.889 3.569 3.626 8.399 27.531 -5.620 2.214 2.770 17.062 -7.365 28.984 11 AA_C13G14:C11G12_BB A 13 ? B 12 ? A 14 ? B 11 ? 1 A G 14 1_555 B C 11 1_555 A C 15 1_555 B G 10 1_555 0.351 -2.264 3.121 -2.654 2.221 28.699 -4.991 -1.246 2.898 4.461 5.329 28.903 12 AA_G14C15:G10C11_BB A 14 ? B 11 ? A 15 ? B 10 ? 1 A C 15 1_555 B G 10 1_555 A C 17 1_555 B G 7 1_555 2.664 -2.595 6.455 9.146 21.336 89.569 -2.608 -1.509 6.061 14.940 -6.404 91.906 13 AA_C15C17:G7G10_BB A 15 ? B 10 ? A 17 ? B 7 ? 1 A C 17 1_555 B G 7 1_555 A G 18 1_555 B U 6 1_555 0.718 -2.584 2.849 -2.414 14.601 13.070 -11.101 -2.685 -0.099 48.118 7.955 19.721 14 AA_C17G18:U6G7_BB A 17 ? B 7 ? A 18 ? B 6 ? 1 A G 18 1_555 B U 6 1_555 A G 19 1_555 B C 5 1_555 -0.597 -1.587 3.293 -1.672 3.668 35.737 -3.086 0.732 3.144 5.953 2.713 35.957 15 AA_G18G19:C5U6_BB A 18 ? B 6 ? A 19 ? B 5 ? 1 A G 19 1_555 B C 5 1_555 A C 20 1_555 B G 4 1_555 -0.557 -1.285 3.154 -3.959 10.598 35.703 -3.289 0.389 2.721 16.774 6.265 37.397 16 AA_G19C20:G4C5_BB A 19 ? B 5 ? A 20 ? B 4 ? 1 A C 20 1_555 B G 4 1_555 A A 21 1_555 B U 3 1_555 0.741 -1.567 3.158 1.079 11.947 33.052 -4.190 -1.084 2.482 20.190 -1.824 35.104 17 AA_C20A21:U3G4_BB A 20 ? B 4 ? A 21 ? B 3 ? 1 A A 21 1_555 B U 3 1_555 A A 22 1_555 B U 2 1_555 -0.783 -0.957 3.176 1.724 5.623 37.827 -2.128 1.399 2.972 8.610 -2.639 38.265 18 AA_A21A22:U2U3_BB A 21 ? B 3 ? A 22 ? B 2 ? 1 A A 22 1_555 B U 2 1_555 A G 23 1_555 B C 1 1_555 0.179 -1.731 3.492 6.179 14.809 29.861 -5.269 0.649 2.385 26.470 -11.045 33.813 19 AA_A22G23:C1U2_BB A 22 ? B 2 ? A 23 ? B 1 ? # _atom_sites.entry_id 2OJ0 _atom_sites.fract_transf_matrix[1][1] 0.023508 _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] 0.020906 _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] 0.017041 _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 C K MN N NA O P # loop_