data_1XPE # _entry.id 1XPE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 1XPE pdb_00001xpe 10.2210/pdb1xpe/pdb NDB UR0046 ? ? RCSB RCSB030610 ? ? WWPDB D_1000030610 ? ? # 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 2005-10-18 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-03-13 # _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' 'Version format compliance' 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_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 23 4 'Structure model' '_pdbx_struct_conn_angle.value' 24 4 'Structure model' '_struct_conn.pdbx_dist_value' 25 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 26 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 33 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_comp_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 1XPE _pdbx_database_status.recvd_initial_deposition_date 2004-10-08 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _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 1JJM . unspecified PDB 1JJN . unspecified PDB 1K9W . unspecified PDB 1XP7 'HIV-1 subtype F' unspecified PDB 1XPF 'HIV-1 subtype A' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ennifar, E.' 1 'Dumas, P.' 2 # _citation.id primary _citation.title 'Polymorphism of Bulged-out Residues in HIV-1 RNA DIS Kissing Complex and Structure Comparison with Solution Studies' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 356 _citation.page_first 771 _citation.page_last 782 _citation.year 2006 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16403527 _citation.pdbx_database_id_DOI 10.1016/j.jmb.2005.12.022 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ennifar, E.' 1 ? primary 'Dumas, P.' 2 ? # 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 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 4 ? ? ? ? 4 non-polymer syn 'SULFATE ION' 96.063 4 ? ? ? ? 5 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 6 water nat water 18.015 121 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'HIV-1 genomic RNA DIS' # _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 'MAGNESIUM ION' MG 3 'SODIUM ION' NA 4 'SULFATE ION' SO4 5 'CHLORIDE ION' CL 6 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 # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C CYT A . n A 1 2 U 2 2 2 U URI A . n A 1 3 U 3 3 3 U URI A . n A 1 4 G 4 4 4 G GUA A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 U 6 6 6 U URI A . n A 1 7 G 7 7 7 G GUA A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 A 9 9 9 A ADE A . n A 1 10 G 10 10 10 G GUA A . n A 1 11 C 11 11 11 C CYT A . n A 1 12 G 12 12 12 G GUA A . n A 1 13 C 13 13 13 C CYT A . n A 1 14 G 14 14 14 G GUA A . n A 1 15 C 15 15 15 C CYT A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 C 17 17 17 C CYT A . n A 1 18 G 18 18 18 G GUA A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 C 20 20 20 C CYT A . n A 1 21 A 21 21 21 A ADE A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 G 23 23 23 G GUA A . n B 1 1 C 1 1 1 C CYT B . n B 1 2 U 2 2 2 U URI B . n B 1 3 U 3 3 3 U URI B . n B 1 4 G 4 4 4 G GUA B . n B 1 5 C 5 5 5 C CYT B . n B 1 6 U 6 6 6 U URI B . n B 1 7 G 7 7 7 G GUA B . n B 1 8 A 8 8 8 A ADE B . n B 1 9 A 9 9 9 A ADE B . n B 1 10 G 10 10 10 G GUA B . n B 1 11 C 11 11 11 C CYT B . n B 1 12 G 12 12 12 G GUA B . n B 1 13 C 13 13 13 C CYT B . n B 1 14 G 14 14 14 G GUA B . n B 1 15 C 15 15 15 C CYT B . n B 1 16 A 16 16 16 A ADE B . n B 1 17 C 17 17 17 C CYT B . n B 1 18 G 18 18 18 G GUA B . n B 1 19 G 19 19 19 G GUA B . n B 1 20 C 20 20 20 C CYT B . n B 1 21 A 21 21 21 A ADE B . n B 1 22 A 22 22 22 A ADE B . n B 1 23 G 23 23 23 G GUA 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 MG 1 101 101 MG MG A . D 3 NA 1 103 103 NA NA A . E 4 SO4 1 108 108 SO4 SO4 A . F 5 CL 1 102 102 CL CL A . G 3 NA 1 111 111 NA NA A . H 4 SO4 1 104 104 SO4 SO4 B . I 3 NA 1 105 105 NA NA B . J 3 NA 1 106 106 NA NA B . K 4 SO4 1 107 107 SO4 SO4 B . L 4 SO4 1 109 109 SO4 SO4 B . M 2 MG 1 110 110 MG MG B . N 6 HOH 1 203 203 HOH WAT A . N 6 HOH 2 204 204 HOH WAT A . N 6 HOH 3 205 205 HOH WAT A . N 6 HOH 4 206 206 HOH WAT A . N 6 HOH 5 211 211 HOH WAT A . N 6 HOH 6 214 214 HOH WAT A . N 6 HOH 7 217 217 HOH WAT A . N 6 HOH 8 221 221 HOH WAT A . N 6 HOH 9 222 222 HOH WAT A . N 6 HOH 10 223 223 HOH WAT A . N 6 HOH 11 224 224 HOH WAT A . N 6 HOH 12 226 226 HOH WAT A . N 6 HOH 13 228 228 HOH WAT A . N 6 HOH 14 232 232 HOH WAT A . N 6 HOH 15 234 234 HOH WAT A . N 6 HOH 16 235 235 HOH WAT A . N 6 HOH 17 239 239 HOH WAT A . N 6 HOH 18 241 241 HOH WAT A . N 6 HOH 19 243 243 HOH WAT A . N 6 HOH 20 244 244 HOH WAT A . N 6 HOH 21 245 245 HOH WAT A . N 6 HOH 22 248 248 HOH WAT A . N 6 HOH 23 249 249 HOH WAT A . N 6 HOH 24 254 254 HOH WAT A . N 6 HOH 25 255 255 HOH WAT A . N 6 HOH 26 258 258 HOH WAT A . N 6 HOH 27 260 260 HOH WAT A . N 6 HOH 28 261 261 HOH WAT A . N 6 HOH 29 262 262 HOH WAT A . N 6 HOH 30 263 263 HOH WAT A . N 6 HOH 31 264 264 HOH WAT A . N 6 HOH 32 271 271 HOH WAT A . N 6 HOH 33 272 272 HOH WAT A . N 6 HOH 34 277 277 HOH WAT A . N 6 HOH 35 278 278 HOH WAT A . N 6 HOH 36 280 280 HOH WAT A . N 6 HOH 37 283 283 HOH WAT A . N 6 HOH 38 287 287 HOH WAT A . N 6 HOH 39 288 288 HOH WAT A . N 6 HOH 40 290 290 HOH WAT A . N 6 HOH 41 292 292 HOH WAT A . N 6 HOH 42 294 294 HOH WAT A . N 6 HOH 43 295 295 HOH WAT A . N 6 HOH 44 299 299 HOH WAT A . N 6 HOH 45 300 300 HOH WAT A . N 6 HOH 46 304 304 HOH WAT A . N 6 HOH 47 305 305 HOH WAT A . N 6 HOH 48 307 307 HOH WAT A . N 6 HOH 49 308 308 HOH WAT A . N 6 HOH 50 311 311 HOH WAT A . N 6 HOH 51 314 314 HOH WAT A . N 6 HOH 52 316 316 HOH WAT A . N 6 HOH 53 318 318 HOH WAT A . N 6 HOH 54 319 319 HOH WAT A . N 6 HOH 55 320 320 HOH WAT A . N 6 HOH 56 321 321 HOH WAT A . O 6 HOH 1 201 201 HOH WAT B . O 6 HOH 2 207 207 HOH WAT B . O 6 HOH 3 208 208 HOH WAT B . O 6 HOH 4 209 209 HOH WAT B . O 6 HOH 5 210 210 HOH WAT B . O 6 HOH 6 212 212 HOH WAT B . O 6 HOH 7 213 213 HOH WAT B . O 6 HOH 8 215 215 HOH WAT B . O 6 HOH 9 216 216 HOH WAT B . O 6 HOH 10 218 218 HOH WAT B . O 6 HOH 11 219 219 HOH WAT B . O 6 HOH 12 220 220 HOH WAT B . O 6 HOH 13 225 225 HOH WAT B . O 6 HOH 14 227 227 HOH WAT B . O 6 HOH 15 229 229 HOH WAT B . O 6 HOH 16 230 230 HOH WAT B . O 6 HOH 17 231 231 HOH WAT B . O 6 HOH 18 233 233 HOH WAT B . O 6 HOH 19 236 236 HOH WAT B . O 6 HOH 20 237 237 HOH WAT B . O 6 HOH 21 238 238 HOH WAT B . O 6 HOH 22 240 240 HOH WAT B . O 6 HOH 23 242 242 HOH WAT B . O 6 HOH 24 246 246 HOH WAT B . O 6 HOH 25 247 247 HOH WAT B . O 6 HOH 26 250 250 HOH WAT B . O 6 HOH 27 251 251 HOH WAT B . O 6 HOH 28 252 252 HOH WAT B . O 6 HOH 29 253 253 HOH WAT B . O 6 HOH 30 256 256 HOH WAT B . O 6 HOH 31 257 257 HOH WAT B . O 6 HOH 32 259 259 HOH WAT B . O 6 HOH 33 265 265 HOH WAT B . O 6 HOH 34 266 266 HOH WAT B . O 6 HOH 35 267 267 HOH WAT B . O 6 HOH 36 268 268 HOH WAT B . O 6 HOH 37 269 269 HOH WAT B . O 6 HOH 38 270 270 HOH WAT B . O 6 HOH 39 273 273 HOH WAT B . O 6 HOH 40 274 274 HOH WAT B . O 6 HOH 41 275 275 HOH WAT B . O 6 HOH 42 276 276 HOH WAT B . O 6 HOH 43 279 279 HOH WAT B . O 6 HOH 44 281 281 HOH WAT B . O 6 HOH 45 282 282 HOH WAT B . O 6 HOH 46 284 284 HOH WAT B . O 6 HOH 47 285 285 HOH WAT B . O 6 HOH 48 286 286 HOH WAT B . O 6 HOH 49 289 289 HOH WAT B . O 6 HOH 50 291 291 HOH WAT B . O 6 HOH 51 293 293 HOH WAT B . O 6 HOH 52 296 296 HOH WAT B . O 6 HOH 53 297 297 HOH WAT B . O 6 HOH 54 298 298 HOH WAT B . O 6 HOH 55 301 301 HOH WAT B . O 6 HOH 56 302 302 HOH WAT B . O 6 HOH 57 303 303 HOH WAT B . O 6 HOH 58 306 306 HOH WAT B . O 6 HOH 59 309 309 HOH WAT B . O 6 HOH 60 310 310 HOH WAT B . O 6 HOH 61 312 312 HOH WAT B . O 6 HOH 62 313 313 HOH WAT B . O 6 HOH 63 315 315 HOH WAT B . O 6 HOH 64 317 317 HOH WAT B . O 6 HOH 65 322 322 HOH WAT B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # _cell.entry_id 1XPE _cell.length_a 27.426 _cell.length_b 114.573 _cell.length_c 95.448 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 1XPE _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1XPE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.53 _exptl_crystal.density_percent_sol 51.33 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'PEG8000, Ammonium sulfate, MgCl2, Na Cacodylate, spermine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K' _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 PEG8000 ? ? ? 1 2 1 'Ammonium sulfate' ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 'Na Cacodylate' ? ? ? 1 5 1 spermine ? ? ? 1 6 2 PEG8000 ? ? ? 1 7 2 'Ammonium sulfate' ? ? ? 1 8 2 MgCl2 ? ? ? 1 9 2 'Na Cacodylate' ? ? ? 1 10 2 spermine ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 90 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _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 0.933 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID14-4' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID14-4 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.933 # _reflns.entry_id 1XPE _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 20 _reflns.d_resolution_high 1.94 _reflns.number_obs 10786 _reflns.number_all ? _reflns.percent_possible_obs 90.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.045 _reflns.pdbx_netI_over_sigmaI 29.6 _reflns.B_iso_Wilson_estimate 26.9 _reflns.pdbx_redundancy 5.8 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.94 _reflns_shell.d_res_low ? _reflns_shell.percent_possible_all 68.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.294 _reflns_shell.meanI_over_sigI_obs 4.1 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1XPE _refine.ls_number_reflns_obs 10468 _refine.ls_number_reflns_all 11605 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF 1055865.24 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.73 _refine.ls_d_res_high 1.94 _refine.ls_percent_reflns_obs 90.2 _refine.ls_R_factor_obs 0.253 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.253 _refine.ls_R_factor_R_free 0.255 _refine.ls_R_factor_R_free_error 0.010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 6.2 _refine.ls_number_reflns_R_free 644 _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 41.3 _refine.aniso_B[1][1] 3.40 _refine.aniso_B[2][2] -4.88 _refine.aniso_B[3][3] 1.48 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.349631 _refine.solvent_model_param_bsol 51.1503 _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 'MOLECULAR REPLACEMENT' _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 1XPE _refine_analyze.Luzzati_coordinate_error_obs 0.33 _refine_analyze.Luzzati_sigma_a_obs 0.31 _refine_analyze.Luzzati_d_res_low_obs 10.00 _refine_analyze.Luzzati_coordinate_error_free 0.35 _refine_analyze.Luzzati_sigma_a_free 0.37 _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 27 _refine_hist.number_atoms_solvent 121 _refine_hist.number_atoms_total 1130 _refine_hist.d_res_high 1.94 _refine_hist.d_res_low 18.73 # 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 0.006 ? ? ? '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 1.2 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 14.0 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.44 ? ? ? '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 1.94 _refine_ls_shell.d_res_low 2.06 _refine_ls_shell.number_reflns_R_work 1353 _refine_ls_shell.R_factor_R_work 0.317 _refine_ls_shell.percent_reflns_obs 77.2 _refine_ls_shell.R_factor_R_free 0.385 _refine_ls_shell.R_factor_R_free_error 0.039 _refine_ls_shell.percent_reflns_R_free 6.8 _refine_ls_shell.number_reflns_R_free 98 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? _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 ION.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 DNA-RNA_REP.PARAM ION.TOP 'X-RAY DIFFRACTION' 4 ION.PARAM SPERMINE.TOP 'X-RAY DIFFRACTION' 5 SPERMINE.PARAM ? 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1XPE _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 1XPE _struct.title 'HIV-1 subtype B genomic RNA Dimerization Initiation Site' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1XPE _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, LOOP-LOOP COMPLEX, HIV-1' # 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 3 ? E N N 4 ? F N N 5 ? G N N 3 ? H N N 4 ? I N N 3 ? J N N 3 ? K N N 4 ? L N N 4 ? M N N 2 ? N N N 6 ? O N N 6 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1XPE _struct_ref.pdbx_db_accession 1XPE _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 1XPE A 1 ? 23 ? 1XPE 1 ? 23 ? 1 23 2 1 1XPE B 1 ? 23 ? 1XPE 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.pdbx_parent_biol_id ? _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 C 1 "O2'" ? ? ? 1_555 G NA . NA ? ? A C 1 A NA 111 1_555 ? ? ? ? ? ? ? 2.791 ? ? metalc2 metalc ? ? A C 1 O2 ? ? ? 1_555 G NA . NA ? ? A C 1 A NA 111 1_555 ? ? ? ? ? ? ? 2.921 ? ? metalc3 metalc ? ? A G 12 N3 ? ? ? 1_555 D NA . NA ? ? A G 12 A NA 103 1_555 ? ? ? ? ? ? ? 2.765 ? ? metalc4 metalc ? ? D NA . NA ? ? ? 1_555 O HOH . O ? ? A NA 103 B HOH 322 1_555 ? ? ? ? ? ? ? 2.631 ? ? metalc5 metalc ? ? B C 1 "O2'" ? ? ? 1_555 J NA . NA ? ? B C 1 B NA 106 1_555 ? ? ? ? ? ? ? 2.994 ? ? metalc6 metalc ? ? B C 1 O2 ? ? ? 1_555 J NA . NA ? ? B C 1 B NA 106 1_555 ? ? ? ? ? ? ? 2.897 ? ? metalc7 metalc ? ? B C 13 O2 ? ? ? 1_555 I NA . NA ? ? B C 13 B NA 105 1_555 ? ? ? ? ? ? ? 2.665 ? ? metalc8 metalc ? ? I NA . NA ? ? ? 1_555 O HOH . O ? ? B NA 105 B HOH 201 1_555 ? ? ? ? ? ? ? 2.790 ? ? metalc9 metalc ? ? J NA . NA ? ? ? 1_555 O HOH . O ? ? B NA 106 B HOH 303 1_555 ? ? ? ? ? ? ? 2.403 ? ? metalc10 metalc ? ? M MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 110 B HOH 220 1_555 ? ? ? ? ? ? ? 2.792 ? ? metalc11 metalc ? ? M MG . MG ? ? ? 1_555 O HOH . O ? ? B MG 110 B HOH 298 1_555 ? ? ? ? ? ? ? 2.794 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 1 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 1 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 1 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 22 N1 ? ? A U 2 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 22 N6 ? ? A U 2 A A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 21 N1 ? ? A U 3 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 21 N6 ? ? A U 3 A A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 4 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 4 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 4 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 19 N1 ? ? A C 5 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 19 O6 ? ? A C 5 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 19 N2 ? ? A C 5 A G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 A G 18 O6 ? ? A U 6 A G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog15 hydrog ? ? A U 6 O2 ? ? ? 1_555 A G 18 N1 ? ? A U 6 A G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 7 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 7 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 7 A 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 ? ? B C 1 N3 ? ? ? 1_555 B G 23 N1 ? ? B C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? B C 1 N4 ? ? ? 1_555 B G 23 O6 ? ? B C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? B C 1 O2 ? ? ? 1_555 B G 23 N2 ? ? B C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? B U 2 N3 ? ? ? 1_555 B A 22 N1 ? ? B U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? B U 2 O4 ? ? ? 1_555 B A 22 N6 ? ? B U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B U 3 N3 ? ? ? 1_555 B A 21 N1 ? ? B U 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? B U 3 O4 ? ? ? 1_555 B A 21 N6 ? ? B U 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? B G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? B G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? B G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? B G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? B G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? B C 5 N3 ? ? ? 1_555 B G 19 N1 ? ? B C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B C 5 N4 ? ? ? 1_555 B G 19 O6 ? ? B C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B C 5 O2 ? ? ? 1_555 B G 19 N2 ? ? B C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B U 6 N3 ? ? ? 1_555 B G 18 O6 ? ? B U 6 B G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog51 hydrog ? ? B U 6 O2 ? ? ? 1_555 B G 18 N1 ? ? B U 6 B G 18 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog52 hydrog ? ? B G 7 N1 ? ? ? 1_555 B C 17 N3 ? ? B G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B G 7 N2 ? ? ? 1_555 B C 17 O2 ? ? B G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B G 7 O6 ? ? ? 1_555 B C 17 N4 ? ? B G 7 B C 17 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 "O2'" ? A C 1 ? A C 1 ? 1_555 NA ? G NA . ? A NA 111 ? 1_555 O2 ? A C 1 ? A C 1 ? 1_555 78.1 ? 2 N3 ? A G 12 ? A G 12 ? 1_555 NA ? D NA . ? A NA 103 ? 1_555 O ? O HOH . ? B HOH 322 ? 1_555 105.1 ? 3 "O2'" ? B C 1 ? B C 1 ? 1_555 NA ? J NA . ? B NA 106 ? 1_555 O2 ? B C 1 ? B C 1 ? 1_555 77.5 ? 4 "O2'" ? B C 1 ? B C 1 ? 1_555 NA ? J NA . ? B NA 106 ? 1_555 O ? O HOH . ? B HOH 303 ? 1_555 122.9 ? 5 O2 ? B C 1 ? B C 1 ? 1_555 NA ? J NA . ? B NA 106 ? 1_555 O ? O HOH . ? B HOH 303 ? 1_555 126.5 ? 6 O2 ? B C 13 ? B C 13 ? 1_555 NA ? I NA . ? B NA 105 ? 1_555 O ? O HOH . ? B HOH 201 ? 1_555 91.3 ? 7 O ? O HOH . ? B HOH 220 ? 1_555 MG ? M MG . ? B MG 110 ? 1_555 O ? O HOH . ? B HOH 298 ? 1_555 79.4 ? # 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 NA 103 ? 3 'BINDING SITE FOR RESIDUE NA A 103' AC2 Software B SO4 104 ? 4 'BINDING SITE FOR RESIDUE SO4 B 104' AC3 Software B NA 105 ? 4 'BINDING SITE FOR RESIDUE NA B 105' AC4 Software B NA 106 ? 3 'BINDING SITE FOR RESIDUE NA B 106' AC5 Software B SO4 107 ? 5 'BINDING SITE FOR RESIDUE SO4 B 107' AC6 Software A SO4 108 ? 3 'BINDING SITE FOR RESIDUE SO4 A 108' AC7 Software B SO4 109 ? 3 'BINDING SITE FOR RESIDUE SO4 B 109' AC8 Software B MG 110 ? 2 'BINDING SITE FOR RESIDUE MG B 110' AC9 Software A CL 102 ? 2 'BINDING SITE FOR RESIDUE CL A 102' BC1 Software A NA 111 ? 4 'BINDING SITE FOR RESIDUE NA A 111' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 3 G A 12 ? G A 12 . ? 1_555 ? 2 AC1 3 G A 14 ? G A 14 . ? 4_566 ? 3 AC1 3 HOH O . ? HOH B 322 . ? 1_555 ? 4 AC2 4 A B 9 ? A B 9 . ? 1_555 ? 5 AC2 4 A B 9 ? A B 9 . ? 3_656 ? 6 AC2 4 HOH O . ? HOH B 289 . ? 1_555 ? 7 AC2 4 HOH O . ? HOH B 289 . ? 3_656 ? 8 AC3 4 G B 12 ? G B 12 . ? 4_566 ? 9 AC3 4 C B 13 ? C B 13 . ? 1_555 ? 10 AC3 4 HOH O . ? HOH B 201 . ? 4_566 ? 11 AC3 4 HOH O . ? HOH B 201 . ? 1_555 ? 12 AC4 3 C B 1 ? C B 1 . ? 1_555 ? 13 AC4 3 U B 2 ? U B 2 . ? 1_555 ? 14 AC4 3 HOH O . ? HOH B 303 . ? 1_555 ? 15 AC5 5 C A 5 ? C A 5 . ? 1_455 ? 16 AC5 5 U A 6 ? U A 6 . ? 1_455 ? 17 AC5 5 A A 16 ? A A 16 . ? 1_555 ? 18 AC5 5 G B 10 ? G B 10 . ? 1_555 ? 19 AC5 5 C B 11 ? C B 11 . ? 1_555 ? 20 AC6 3 C A 1 ? C A 1 . ? 1_555 ? 21 AC6 3 HOH N . ? HOH A 239 . ? 1_555 ? 22 AC6 3 HOH O . ? HOH B 246 . ? 5_555 ? 23 AC7 3 HOH N . ? HOH A 311 . ? 5_445 ? 24 AC7 3 C B 1 ? C B 1 . ? 1_555 ? 25 AC7 3 HOH O . ? HOH B 238 . ? 1_555 ? 26 AC8 2 HOH O . ? HOH B 220 . ? 1_555 ? 27 AC8 2 HOH O . ? HOH B 298 . ? 1_555 ? 28 AC9 2 C A 13 ? C A 13 . ? 1_555 ? 29 AC9 2 HOH N . ? HOH A 278 . ? 1_555 ? 30 BC1 4 C A 1 ? C A 1 . ? 1_555 ? 31 BC1 4 U A 2 ? U A 2 . ? 1_555 ? 32 BC1 4 G B 23 ? G B 23 . ? 5_555 ? 33 BC1 4 HOH O . ? HOH B 302 . ? 5_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C2'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 22 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 22 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 22 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 129.74 _pdbx_validate_rmsd_angle.angle_target_value 113.70 _pdbx_validate_rmsd_angle.angle_deviation 16.04 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.60 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 2 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.076 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 205 ? N HOH . 2 1 A HOH 234 ? N HOH . 3 1 B HOH 201 ? O HOH . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CL CL CL N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 MG MG MG N N 115 NA NA NA N N 116 SO4 S S N N 117 SO4 O1 O N N 118 SO4 O2 O N N 119 SO4 O3 O N N 120 SO4 O4 O N N 121 U OP3 O N N 122 U P P N N 123 U OP1 O N N 124 U OP2 O N N 125 U "O5'" O N N 126 U "C5'" C N N 127 U "C4'" C N R 128 U "O4'" O N N 129 U "C3'" C N S 130 U "O3'" O N N 131 U "C2'" C N R 132 U "O2'" O N N 133 U "C1'" C N R 134 U N1 N N N 135 U C2 C N N 136 U O2 O N N 137 U N3 N N N 138 U C4 C N N 139 U O4 O N N 140 U C5 C N N 141 U C6 C N N 142 U HOP3 H N N 143 U HOP2 H N N 144 U "H5'" H N N 145 U "H5''" H N N 146 U "H4'" H N N 147 U "H3'" H N N 148 U "HO3'" H N N 149 U "H2'" H N N 150 U "HO2'" H N N 151 U "H1'" H N N 152 U H3 H N N 153 U H5 H N N 154 U H6 H N N 155 # 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 SO4 S O1 doub N N 118 SO4 S O2 doub N N 119 SO4 S O3 sing N N 120 SO4 S O4 sing N N 121 U OP3 P sing N N 122 U OP3 HOP3 sing N N 123 U P OP1 doub N N 124 U P OP2 sing N N 125 U P "O5'" sing N N 126 U OP2 HOP2 sing N N 127 U "O5'" "C5'" sing N N 128 U "C5'" "C4'" sing N N 129 U "C5'" "H5'" sing N N 130 U "C5'" "H5''" sing N N 131 U "C4'" "O4'" sing N N 132 U "C4'" "C3'" sing N N 133 U "C4'" "H4'" sing N N 134 U "O4'" "C1'" sing N N 135 U "C3'" "O3'" sing N N 136 U "C3'" "C2'" sing N N 137 U "C3'" "H3'" sing N N 138 U "O3'" "HO3'" sing N N 139 U "C2'" "O2'" sing N N 140 U "C2'" "C1'" sing N N 141 U "C2'" "H2'" sing N N 142 U "O2'" "HO2'" sing N N 143 U "C1'" N1 sing N N 144 U "C1'" "H1'" sing N N 145 U N1 C2 sing N N 146 U N1 C6 sing N N 147 U C2 O2 doub N N 148 U C2 N3 sing N N 149 U N3 C4 sing N N 150 U N3 H3 sing N N 151 U C4 O4 doub N N 152 U C4 C5 sing N N 153 U C5 C6 doub N N 154 U C5 H5 sing N N 155 U C6 H6 sing N N 156 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1XPE 'double helix' 1XPE 'a-form double helix' 1XPE 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A C 1 1_555 A G 23 1_555 0.182 -0.257 0.207 5.873 -18.017 -2.217 1 A_C1:G23_A A 1 ? A 23 ? 19 1 1 A U 2 1_555 A A 22 1_555 0.163 -0.134 0.298 -3.273 -19.503 0.178 2 A_U2:A22_A A 2 ? A 22 ? 20 1 1 A U 3 1_555 A A 21 1_555 0.251 -0.132 -0.018 2.428 -13.975 4.653 3 A_U3:A21_A A 3 ? A 21 ? 20 1 1 A G 4 1_555 A C 20 1_555 0.364 -0.196 0.016 1.145 -17.691 2.628 4 A_G4:C20_A A 4 ? A 20 ? 19 1 1 A C 5 1_555 A G 19 1_555 0.490 -0.388 0.242 3.739 -17.587 1.511 5 A_C5:G19_A A 5 ? A 19 ? 19 1 1 A U 6 1_555 A G 18 1_555 2.249 -0.530 0.136 -0.909 -23.424 6.731 6 A_U6:G18_A A 6 ? A 18 ? 28 1 1 A G 7 1_555 A C 17 1_555 -0.156 -0.216 0.063 0.427 -8.673 -1.903 7 A_G7:C17_A A 7 ? A 17 ? 19 1 1 B G 10 1_555 A C 15 1_555 -0.378 -0.200 -0.267 -13.995 -14.027 2.274 8 B_G10:C15_A B 10 ? A 15 ? 19 1 1 B C 11 1_555 A G 14 1_555 -0.054 -0.165 0.199 -7.005 -11.844 -1.489 9 B_C11:G14_A B 11 ? A 14 ? 19 1 1 B G 12 1_555 A C 13 1_555 0.016 -0.125 -0.060 -4.734 -12.122 0.163 10 B_G12:C13_A B 12 ? A 13 ? 19 1 1 B C 13 1_555 A G 12 1_555 0.170 -0.177 0.036 3.706 -11.533 0.601 11 B_C13:G12_A B 13 ? A 12 ? 19 1 1 B G 14 1_555 A C 11 1_555 -0.207 -0.291 0.151 4.374 -12.073 -0.514 12 B_G14:C11_A B 14 ? A 11 ? 19 1 1 B C 15 1_555 A G 10 1_555 0.467 -0.266 -0.016 4.805 -9.521 1.951 13 B_C15:G10_A B 15 ? A 10 ? 19 1 1 B C 17 1_555 B G 7 1_555 0.006 -0.248 0.107 -0.632 -10.956 0.112 14 B_C17:G7_B B 17 ? B 7 ? 19 1 1 B G 18 1_555 B U 6 1_555 -2.107 -0.454 -0.107 2.494 -23.620 7.895 15 B_G18:U6_B B 18 ? B 6 ? 28 1 1 B G 19 1_555 B C 5 1_555 -0.194 -0.269 0.116 -6.935 -16.515 3.779 16 B_G19:C5_B B 19 ? B 5 ? 19 1 1 B C 20 1_555 B G 4 1_555 0.575 -0.220 0.050 -1.516 -12.754 4.972 17 B_C20:G4_B B 20 ? B 4 ? 19 1 1 B A 21 1_555 B U 3 1_555 -0.199 -0.261 0.273 -3.512 -11.392 3.081 18 B_A21:U3_B B 21 ? B 3 ? 20 1 1 B A 22 1_555 B U 2 1_555 -0.069 -0.148 0.136 -0.807 -14.900 1.954 19 B_A22:U2_B B 22 ? B 2 ? 20 1 1 B G 23 1_555 B C 1 1_555 -0.236 -0.256 0.229 -9.287 -16.439 -2.217 20 B_G23:C1_B B 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 A G 23 1_555 A U 2 1_555 A A 22 1_555 -0.447 -1.573 3.408 -4.008 7.766 34.357 -3.726 0.146 3.023 12.889 6.652 35.419 1 AA_C1U2:A22G23_AA A 1 ? A 23 ? A 2 ? A 22 ? 1 A U 2 1_555 A A 22 1_555 A U 3 1_555 A A 21 1_555 -0.158 -1.138 3.009 -0.100 4.868 34.640 -2.552 0.249 2.828 8.126 0.167 34.970 2 AA_U2U3:A21A22_AA A 2 ? A 22 ? A 3 ? A 21 ? 1 A U 3 1_555 A A 21 1_555 A G 4 1_555 A C 20 1_555 -0.638 -1.477 3.221 -2.108 12.577 28.212 -4.968 0.829 2.399 24.293 4.071 30.907 3 AA_U3G4:C20A21_AA A 3 ? A 21 ? A 4 ? A 20 ? 1 A G 4 1_555 A C 20 1_555 A C 5 1_555 A G 19 1_555 0.111 -1.540 3.203 -1.999 3.997 32.645 -3.364 -0.520 2.986 7.070 3.536 32.941 4 AA_G4C5:G19C20_AA A 4 ? A 20 ? A 5 ? A 19 ? 1 A C 5 1_555 A G 19 1_555 A U 6 1_555 A G 18 1_555 0.921 -1.779 3.412 6.031 0.889 36.421 -2.938 -0.590 3.472 1.410 -9.567 36.911 5 AA_C5U6:G18G19_AA A 5 ? A 19 ? A 6 ? A 18 ? 1 A U 6 1_555 A G 18 1_555 A G 7 1_555 A C 17 1_555 -0.554 -1.825 2.819 4.690 19.095 21.628 -6.316 1.762 0.833 41.493 -10.192 29.151 6 AA_U6G7:C17G18_AA A 6 ? A 18 ? A 7 ? A 17 ? 1 A G 7 1_555 A C 17 1_555 B G 10 1_555 A C 15 1_555 -2.113 -2.812 6.553 -0.402 15.327 85.819 -2.701 1.519 6.095 11.179 0.293 86.915 7 AB_G7G10:C15C17_AA A 7 ? A 17 ? B 10 ? A 15 ? 1 B G 10 1_555 A C 15 1_555 B C 11 1_555 A G 14 1_555 -0.493 -1.232 3.075 -4.585 3.707 33.173 -2.688 0.157 2.963 6.430 7.952 33.678 8 BB_G10C11:G14C15_AA B 10 ? A 15 ? B 11 ? A 14 ? 1 B C 11 1_555 A G 14 1_555 B G 12 1_555 A C 13 1_555 -0.133 -1.789 3.096 2.059 12.980 30.032 -5.055 0.534 2.146 23.674 -3.755 32.721 9 BB_C11G12:C13G14_AA B 11 ? A 14 ? B 12 ? A 13 ? 1 B G 12 1_555 A C 13 1_555 B C 13 1_555 A G 12 1_555 0.015 -0.872 3.101 0.766 6.449 30.727 -2.729 0.104 2.863 12.002 -1.425 31.390 10 BB_G12C13:G12C13_AA B 12 ? A 13 ? B 13 ? A 12 ? 1 B C 13 1_555 A G 12 1_555 B G 14 1_555 A C 11 1_555 0.588 -1.776 3.050 -1.389 13.761 28.545 -5.316 -1.286 1.975 26.063 2.630 31.656 11 BB_C13G14:C11G12_AA B 13 ? A 12 ? B 14 ? A 11 ? 1 B G 14 1_555 A C 11 1_555 B C 15 1_555 A G 10 1_555 0.134 -1.607 3.265 0.455 2.172 36.764 -2.834 -0.151 3.170 3.440 -0.720 36.829 12 BB_G14C15:G10C11_AA B 14 ? A 11 ? B 15 ? A 10 ? 1 B C 15 1_555 A G 10 1_555 B C 17 1_555 B G 7 1_555 1.924 -3.106 6.148 2.553 15.965 81.176 -3.074 -1.344 5.619 12.161 -1.945 82.496 13 BB_C15C17:G7G10_BA B 15 ? A 10 ? B 17 ? B 7 ? 1 B C 17 1_555 B G 7 1_555 B G 18 1_555 B U 6 1_555 0.471 -1.645 2.888 -3.229 18.335 23.121 -5.965 -1.405 1.209 38.683 6.812 29.605 14 BB_C17G18:U6G7_BB B 17 ? B 7 ? B 18 ? B 6 ? 1 B G 18 1_555 B U 6 1_555 B G 19 1_555 B C 5 1_555 -0.685 -1.412 3.492 -7.280 7.106 39.345 -2.867 0.135 3.270 10.346 10.599 40.588 15 BB_G18G19:C5U6_BB B 18 ? B 6 ? B 19 ? B 5 ? 1 B G 19 1_555 B C 5 1_555 B C 20 1_555 B G 4 1_555 0.062 -1.346 3.152 0.926 2.123 35.969 -2.463 0.024 3.071 3.433 -1.498 36.041 16 BB_G19C20:G4C5_BB B 19 ? B 5 ? B 20 ? B 4 ? 1 B C 20 1_555 B G 4 1_555 B A 21 1_555 B U 3 1_555 0.019 -1.548 3.060 0.101 13.406 26.355 -5.399 -0.020 2.048 27.272 -0.205 29.515 17 BB_C20A21:U3G4_BB B 20 ? B 4 ? B 21 ? B 3 ? 1 B A 21 1_555 B U 3 1_555 B A 22 1_555 B U 2 1_555 0.203 -1.124 3.162 3.111 3.171 34.165 -2.368 0.120 3.055 5.369 -5.267 34.444 18 BB_A21A22:U2U3_BB B 21 ? B 3 ? B 22 ? B 2 ? 1 B A 22 1_555 B U 2 1_555 B G 23 1_555 B C 1 1_555 0.276 -1.777 3.310 1.479 10.423 33.740 -4.375 -0.250 2.670 17.438 -2.475 35.299 19 BB_A22G23:C1U2_BB B 22 ? B 2 ? B 23 ? B 1 ? # _atom_sites.entry_id 1XPE _atom_sites.fract_transf_matrix[1][1] 0.036462 _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] 0.008728 _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] 0.010477 _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 CL MG N NA O P S # loop_