data_1DPL # _entry.id 1DPL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 1DPL pdb_00001dpl 10.2210/pdb1dpl/pdb NDB AD0007 ? ? RCSB RCSB010269 ? ? WWPDB D_1000010269 ? ? # 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 2000-04-04 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2022-06-22 5 'Structure model' 2 1 2024-02-07 # _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' 6 4 'Structure model' 'Polymer sequence' 7 5 'Structure model' 'Data collection' # 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 2 4 'Structure model' database_2 3 4 'Structure model' entity_poly 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' pdbx_struct_mod_residue 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site 8 5 'Structure model' chem_comp_atom 9 5 'Structure model' chem_comp_bond # 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' '_chem_comp.mon_nstd_flag' 2 4 'Structure model' '_chem_comp.type' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.value' 9 4 'Structure model' '_struct_conn.conn_type_id' 10 4 'Structure model' '_struct_conn.id' 11 4 'Structure model' '_struct_conn.pdbx_dist_value' 12 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 13 4 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 14 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 15 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 16 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 21 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 23 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 28 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 29 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 30 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DPL _pdbx_database_status.recvd_initial_deposition_date 1999-12-27 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Egli, M.' 1 'Tereshko, V.' 2 'Teplova, M.' 3 'Minasov, G.' 4 'Joachimiak, A.' 5 'Sanishvili, R.' 6 'Weeks, C.M.' 7 'Miller, R.' 8 'Maier, M.A.' 9 'An, H.' 10 'Dan Cook, P.' 11 'Manoharan, M.' 12 # _citation.id primary _citation.title 'X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution.' _citation.journal_abbrev Biopolymers _citation.journal_volume 48 _citation.page_first 234 _citation.page_last 252 _citation.year 1998 _citation.journal_id_ASTM BIPMAA _citation.country US _citation.journal_id_ISSN 0006-3525 _citation.journal_id_CSD 0161 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10699842 _citation.pdbx_database_id_DOI '10.1002/(SICI)1097-0282(1998)48:4<234::AID-BIP4>3.0.CO;2-H' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Tereshko, V.' 2 ? primary 'Teplova, M.' 3 ? primary 'Minasov, G.' 4 ? primary 'Joachimiak, A.' 5 ? primary 'Sanishvili, R.' 6 ? primary 'Weeks, C.M.' 7 ? primary 'Miller, R.' 8 ? primary 'Maier, M.A.' 9 ? primary 'An, H.' 10 ? primary 'Dan Cook, P.' 11 ? primary 'Manoharan, M.' 12 ? # 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'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'" 3073.059 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 non-polymer syn SPERMINE 202.340 2 ? ? ? ? 4 water nat water 18.015 177 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(T23)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTAXACGC _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 SPERMINE SPM 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 T23 n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 T23 non-polymer . "2'-O-METHYL-3'-METHYL-3'-DEOXY-ARABINOFURANOSYL-THYMINE-5'-PHOSPHATE" ? 'C12 H19 N2 O8 P' 350.262 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 T23 6 6 6 T23 T23 A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 T23 6 16 16 T23 T23 B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C 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 1 301 301 MG MG A . D 3 SPM 1 221 221 SPM SPM B . E 3 SPM 1 222 222 SPM SPM B . F 2 MG 1 1301 1301 MG MG B . G 4 HOH 1 302 302 HOH HOH A . G 4 HOH 2 305 305 HOH HOH A . G 4 HOH 3 306 306 HOH HOH A . G 4 HOH 4 307 307 HOH HOH A . G 4 HOH 5 310 310 HOH HOH A . G 4 HOH 6 313 313 HOH HOH A . G 4 HOH 7 315 315 HOH HOH A . G 4 HOH 8 317 317 HOH HOH A . G 4 HOH 9 318 318 HOH HOH A . G 4 HOH 10 319 319 HOH HOH A . G 4 HOH 11 320 320 HOH HOH A . G 4 HOH 12 323 323 HOH HOH A . G 4 HOH 13 324 324 HOH HOH A . G 4 HOH 14 328 328 HOH HOH A . G 4 HOH 15 329 329 HOH HOH A . G 4 HOH 16 331 331 HOH HOH A . G 4 HOH 17 333 333 HOH HOH A . G 4 HOH 18 334 334 HOH HOH A . G 4 HOH 19 335 335 HOH HOH A . G 4 HOH 20 336 336 HOH HOH A . G 4 HOH 21 338 338 HOH HOH A . G 4 HOH 22 341 341 HOH HOH A . G 4 HOH 23 343 343 HOH HOH A . G 4 HOH 24 345 345 HOH HOH A . G 4 HOH 25 349 349 HOH HOH A . G 4 HOH 26 353 353 HOH HOH A . G 4 HOH 27 358 358 HOH HOH A . G 4 HOH 28 359 359 HOH HOH A . G 4 HOH 29 361 361 HOH HOH A . G 4 HOH 30 364 364 HOH HOH A . G 4 HOH 31 365 365 HOH HOH A . G 4 HOH 32 368 368 HOH HOH A . G 4 HOH 33 370 370 HOH HOH A . G 4 HOH 34 373 373 HOH HOH A . G 4 HOH 35 374 374 HOH HOH A . G 4 HOH 36 375 375 HOH HOH A . G 4 HOH 37 376 376 HOH HOH A . G 4 HOH 38 377 377 HOH HOH A . G 4 HOH 39 379 379 HOH HOH A . G 4 HOH 40 380 380 HOH HOH A . G 4 HOH 41 381 381 HOH HOH A . G 4 HOH 42 388 388 HOH HOH A . G 4 HOH 43 389 389 HOH HOH A . G 4 HOH 44 390 390 HOH HOH A . G 4 HOH 45 397 397 HOH HOH A . G 4 HOH 46 399 399 HOH HOH A . G 4 HOH 47 401 401 HOH HOH A . G 4 HOH 48 404 404 HOH HOH A . G 4 HOH 49 407 407 HOH HOH A . G 4 HOH 50 409 409 HOH HOH A . G 4 HOH 51 410 410 HOH HOH A . G 4 HOH 52 411 411 HOH HOH A . G 4 HOH 53 412 412 HOH HOH A . G 4 HOH 54 415 415 HOH HOH A . G 4 HOH 55 416 416 HOH HOH A . G 4 HOH 56 418 418 HOH HOH A . G 4 HOH 57 420 420 HOH HOH A . G 4 HOH 58 421 421 HOH HOH A . G 4 HOH 59 423 423 HOH HOH A . G 4 HOH 60 424 424 HOH HOH A . G 4 HOH 61 426 426 HOH HOH A . G 4 HOH 62 427 427 HOH HOH A . G 4 HOH 63 431 431 HOH HOH A . G 4 HOH 64 434 434 HOH HOH A . G 4 HOH 65 435 435 HOH HOH A . G 4 HOH 66 441 441 HOH HOH A . G 4 HOH 67 442 442 HOH HOH A . G 4 HOH 68 443 443 HOH HOH A . G 4 HOH 69 444 444 HOH HOH A . G 4 HOH 70 451 451 HOH HOH A . G 4 HOH 71 454 454 HOH HOH A . G 4 HOH 72 459 459 HOH HOH A . G 4 HOH 73 460 460 HOH HOH A . G 4 HOH 74 462 462 HOH HOH A . G 4 HOH 75 464 464 HOH HOH A . G 4 HOH 76 472 472 HOH HOH A . G 4 HOH 77 473 473 HOH HOH A . G 4 HOH 78 474 474 HOH HOH A . G 4 HOH 79 475 475 HOH HOH A . G 4 HOH 80 476 476 HOH HOH A . G 4 HOH 81 479 479 HOH HOH A . G 4 HOH 82 494 494 HOH HOH A . G 4 HOH 83 498 498 HOH HOH A . G 4 HOH 84 502 502 HOH HOH A . G 4 HOH 85 1221 1221 HOH HOH A . G 4 HOH 86 1342 1342 HOH HOH A . G 4 HOH 87 1352 1352 HOH HOH A . G 4 HOH 88 1354 1354 HOH HOH A . G 4 HOH 89 1403 1403 HOH HOH A . G 4 HOH 90 1405 1405 HOH HOH A . G 4 HOH 91 1425 1425 HOH HOH A . G 4 HOH 92 1428 1428 HOH HOH A . G 4 HOH 93 1440 1440 HOH HOH A . G 4 HOH 94 1452 1452 HOH HOH A . G 4 HOH 95 1461 1461 HOH HOH A . G 4 HOH 96 2001 2001 HOH HOH A . G 4 HOH 97 2455 2455 HOH HOH A . H 4 HOH 1 303 303 HOH HOH B . H 4 HOH 2 304 304 HOH HOH B . H 4 HOH 3 308 308 HOH HOH B . H 4 HOH 4 309 309 HOH HOH B . H 4 HOH 5 311 311 HOH HOH B . H 4 HOH 6 312 312 HOH HOH B . H 4 HOH 7 314 314 HOH HOH B . H 4 HOH 8 316 316 HOH HOH B . H 4 HOH 9 321 321 HOH HOH B . H 4 HOH 10 322 322 HOH HOH B . H 4 HOH 11 325 325 HOH HOH B . H 4 HOH 12 326 326 HOH HOH B . H 4 HOH 13 327 327 HOH HOH B . H 4 HOH 14 330 330 HOH HOH B . H 4 HOH 15 332 332 HOH HOH B . H 4 HOH 16 337 337 HOH HOH B . H 4 HOH 17 339 339 HOH HOH B . H 4 HOH 18 340 340 HOH HOH B . H 4 HOH 19 344 344 HOH HOH B . H 4 HOH 20 347 347 HOH HOH B . H 4 HOH 21 348 348 HOH HOH B . H 4 HOH 22 350 350 HOH HOH B . H 4 HOH 23 351 351 HOH HOH B . H 4 HOH 24 356 356 HOH HOH B . H 4 HOH 25 357 357 HOH HOH B . H 4 HOH 26 360 360 HOH HOH B . H 4 HOH 27 362 362 HOH HOH B . H 4 HOH 28 363 363 HOH HOH B . H 4 HOH 29 366 366 HOH HOH B . H 4 HOH 30 367 367 HOH HOH B . H 4 HOH 31 369 369 HOH HOH B . H 4 HOH 32 371 371 HOH HOH B . H 4 HOH 33 372 372 HOH HOH B . H 4 HOH 34 378 378 HOH HOH B . H 4 HOH 35 382 382 HOH HOH B . H 4 HOH 36 383 383 HOH HOH B . H 4 HOH 37 384 384 HOH HOH B . H 4 HOH 38 385 385 HOH HOH B . H 4 HOH 39 386 386 HOH HOH B . H 4 HOH 40 387 387 HOH HOH B . H 4 HOH 41 391 391 HOH HOH B . H 4 HOH 42 392 392 HOH HOH B . H 4 HOH 43 393 393 HOH HOH B . H 4 HOH 44 394 394 HOH HOH B . H 4 HOH 45 395 395 HOH HOH B . H 4 HOH 46 396 396 HOH HOH B . H 4 HOH 47 400 400 HOH HOH B . H 4 HOH 48 406 406 HOH HOH B . H 4 HOH 49 417 417 HOH HOH B . H 4 HOH 50 422 422 HOH HOH B . H 4 HOH 51 429 429 HOH HOH B . H 4 HOH 52 432 432 HOH HOH B . H 4 HOH 53 445 445 HOH HOH B . H 4 HOH 54 446 446 HOH HOH B . H 4 HOH 55 447 447 HOH HOH B . H 4 HOH 56 448 448 HOH HOH B . H 4 HOH 57 449 449 HOH HOH B . H 4 HOH 58 450 450 HOH HOH B . H 4 HOH 59 455 455 HOH HOH B . H 4 HOH 60 456 456 HOH HOH B . H 4 HOH 61 457 457 HOH HOH B . H 4 HOH 62 458 458 HOH HOH B . H 4 HOH 63 469 469 HOH HOH B . H 4 HOH 64 470 470 HOH HOH B . H 4 HOH 65 471 471 HOH HOH B . H 4 HOH 66 481 481 HOH HOH B . H 4 HOH 67 482 482 HOH HOH B . H 4 HOH 68 485 485 HOH HOH B . H 4 HOH 69 486 486 HOH HOH B . H 4 HOH 70 493 493 HOH HOH B . H 4 HOH 71 496 496 HOH HOH B . H 4 HOH 72 1222 1222 HOH HOH B . H 4 HOH 73 1302 1302 HOH HOH B . H 4 HOH 74 1303 1303 HOH HOH B . H 4 HOH 75 1304 1304 HOH HOH B . H 4 HOH 76 1305 1305 HOH HOH B . H 4 HOH 77 1306 1306 HOH HOH B . H 4 HOH 78 1307 1307 HOH HOH B . H 4 HOH 79 1355 1355 HOH HOH B . H 4 HOH 80 1398 1398 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 1 B SPM 222 ? N1 ? E SPM 1 N1 2 1 N 1 B SPM 222 ? C2 ? E SPM 1 C2 3 1 N 1 B SPM 222 ? C3 ? E SPM 1 C3 4 1 N 1 B SPM 222 ? N14 ? E SPM 1 N14 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 SHELXS phasing . ? 3 SHELXL-97 refinement . ? 4 # _cell.entry_id 1DPL _cell.length_a 24.627 _cell.length_b 42.717 _cell.length_c 46.906 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DPL _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 # _exptl.entry_id 1DPL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 36.17 _exptl_crystal.density_Matthews 1.93 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'SPERMINE, MGCL2, NACL, KCL, SODIUM CACODYLATE BUFFER, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 SPERMINE ? ? ? 1 2 1 'SODIUM CACODYLATE BUFFER' ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 NACL ? ? ? 1 5 1 KCL ? ? ? 1 6 2 MGCL2 ? ? ? 1 7 2 NACL ? ? ? 1 8 2 KCL ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _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 1999-06-15 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.800 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength 0.800 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1DPL _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 0.83 _reflns.number_obs 47403 _reflns.number_all 47403 _reflns.percent_possible_obs 99.7 _reflns.pdbx_Rmerge_I_obs 0.049 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.8 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 0.83 _reflns_shell.d_res_low 0.90 _reflns_shell.percent_possible_all 98.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1DPL _refine.ls_number_reflns_obs 47403 _refine.ls_number_reflns_all 47403 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20 _refine.ls_d_res_high 0.83 _refine.ls_percent_reflns_obs 99.7 _refine.ls_R_factor_obs 0.117 _refine.ls_R_factor_all 0.117 _refine.ls_R_factor_R_work 0.115 _refine.ls_R_factor_R_free 0.121 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10 _refine.ls_number_reflns_R_free 4742 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'PARKINSON ET AL.' _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.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_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 447 _refine_hist.pdbx_number_atoms_ligand 26 _refine_hist.number_atoms_solvent 177 _refine_hist.number_atoms_total 650 _refine_hist.d_res_high 0.83 _refine_hist.d_res_low 20 # 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 s_bond_d 0.037 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.019 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1DPL _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 1DPL _struct.title ;A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DPL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'MODIFIED A-DECAMER AT 0.83 A RESOLUTION, DEOXYRIBONUCLEIC ACID, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 2 ? G N N 4 ? H N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1DPL _struct_ref.pdbx_db_accession 1DPL _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 1DPL A 1 ? 10 ? 1DPL 1 ? 10 ? 1 10 2 1 1DPL B 1 ? 10 ? 1DPL 11 ? 20 ? 11 20 # _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 # _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 covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A T23 6 P ? ? A DA 5 A T23 6 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale2 covale one ? A T23 6 C3M ? ? ? 1_555 A DA 7 P ? ? A T23 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.743 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B T23 6 P ? ? B DA 15 B T23 16 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale4 covale one ? B T23 6 C3M ? ? ? 1_555 B DA 7 P ? ? B T23 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.739 ? ? covale5 covale none ? B DG 9 OP1 B ? ? 1_555 E SPM . N5 ? ? B DG 19 B SPM 222 1_555 ? ? ? ? ? ? ? 1.796 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 301 A HOH 302 1_555 ? ? ? ? ? ? ? 2.068 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 301 A HOH 305 1_555 ? ? ? ? ? ? ? 2.111 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 301 A HOH 306 1_555 ? ? ? ? ? ? ? 2.027 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 301 A HOH 307 1_555 ? ? ? ? ? ? ? 2.085 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 301 B HOH 303 1_555 ? ? ? ? ? ? ? 2.090 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 301 B HOH 304 1_555 ? ? ? ? ? ? ? 2.052 ? ? metalc7 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1301 B HOH 1302 1_555 ? ? ? ? ? ? ? 2.119 ? ? metalc8 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1301 B HOH 1303 1_555 ? ? ? ? ? ? ? 2.053 ? ? metalc9 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1301 B HOH 1304 1_555 ? ? ? ? ? ? ? 1.832 ? ? metalc10 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1301 B HOH 1305 1_555 ? ? ? ? ? ? ? 2.042 ? ? metalc11 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1301 B HOH 1306 1_555 ? ? ? ? ? ? ? 2.134 ? ? metalc12 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 1301 B HOH 1307 1_555 ? ? ? ? ? ? ? 2.143 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B T23 6 N3 ? ? A DA 5 B T23 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B T23 6 O4 ? ? A DA 5 B T23 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A T23 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A T23 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A T23 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A T23 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? G HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? G HOH . ? A HOH 305 ? 1_555 91.0 ? 2 O ? G HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? G HOH . ? A HOH 306 ? 1_555 88.3 ? 3 O ? G HOH . ? A HOH 305 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? G HOH . ? A HOH 306 ? 1_555 92.3 ? 4 O ? G HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? G HOH . ? A HOH 307 ? 1_555 92.6 ? 5 O ? G HOH . ? A HOH 305 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? G HOH . ? A HOH 307 ? 1_555 176.5 ? 6 O ? G HOH . ? A HOH 306 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? G HOH . ? A HOH 307 ? 1_555 87.7 ? 7 O ? G HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 303 ? 1_555 177.5 ? 8 O ? G HOH . ? A HOH 305 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 303 ? 1_555 90.5 ? 9 O ? G HOH . ? A HOH 306 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 303 ? 1_555 93.6 ? 10 O ? G HOH . ? A HOH 307 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 303 ? 1_555 85.9 ? 11 O ? G HOH . ? A HOH 302 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 304 ? 1_555 91.1 ? 12 O ? G HOH . ? A HOH 305 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 304 ? 1_555 89.1 ? 13 O ? G HOH . ? A HOH 306 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 304 ? 1_555 178.5 ? 14 O ? G HOH . ? A HOH 307 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 304 ? 1_555 90.9 ? 15 O ? H HOH . ? B HOH 303 ? 1_555 MG ? C MG . ? A MG 301 ? 1_555 O ? H HOH . ? B HOH 304 ? 1_555 86.9 ? 16 O ? H HOH . ? B HOH 1302 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1303 ? 1_555 95.8 ? 17 O ? H HOH . ? B HOH 1302 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1304 ? 1_555 89.0 ? 18 O ? H HOH . ? B HOH 1303 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1304 ? 1_555 100.3 ? 19 O ? H HOH . ? B HOH 1302 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1305 ? 1_555 93.8 ? 20 O ? H HOH . ? B HOH 1303 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1305 ? 1_555 85.7 ? 21 O ? H HOH . ? B HOH 1304 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1305 ? 1_555 173.1 ? 22 O ? H HOH . ? B HOH 1302 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1306 ? 1_555 159.8 ? 23 O ? H HOH . ? B HOH 1303 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1306 ? 1_555 99.8 ? 24 O ? H HOH . ? B HOH 1304 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1306 ? 1_555 100.5 ? 25 O ? H HOH . ? B HOH 1305 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1306 ? 1_555 74.8 ? 26 O ? H HOH . ? B HOH 1302 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1307 ? 1_555 83.7 ? 27 O ? H HOH . ? B HOH 1303 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1307 ? 1_555 175.6 ? 28 O ? H HOH . ? B HOH 1304 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1307 ? 1_555 84.1 ? 29 O ? H HOH . ? B HOH 1305 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1307 ? 1_555 90.0 ? 30 O ? H HOH . ? B HOH 1306 ? 1_555 MG ? F MG . ? B MG 1301 ? 1_555 O ? H HOH . ? B HOH 1307 ? 1_555 79.7 ? # 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 B SPM 221 ? 11 'BINDING SITE FOR RESIDUE SPM B 221' AC2 Software B SPM 222 ? 9 'BINDING SITE FOR RESIDUE SPM B 222' AC3 Software A MG 301 ? 6 'BINDING SITE FOR RESIDUE MG A 301' AC4 Software B MG 1301 ? 6 'BINDING SITE FOR RESIDUE MG B 1301' # 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 11 DG A 9 ? DG A 9 . ? 4_456 ? 2 AC1 11 HOH G . ? HOH A 329 . ? 2_555 ? 3 AC1 11 HOH G . ? HOH A 341 . ? 4_456 ? 4 AC1 11 HOH G . ? HOH A 358 . ? 2_555 ? 5 AC1 11 HOH G . ? HOH A 502 . ? 2_555 ? 6 AC1 11 DG B 3 ? DG B 13 . ? 1_555 ? 7 AC1 11 DT B 4 ? DT B 14 . ? 1_555 ? 8 AC1 11 DC B 8 ? DC B 18 . ? 2_455 ? 9 AC1 11 DG B 9 ? DG B 19 . ? 2_455 ? 10 AC1 11 HOH H . ? HOH B 470 . ? 2_455 ? 11 AC1 11 HOH H . ? HOH B 1222 . ? 1_555 ? 12 AC2 9 HOH G . ? HOH A 336 . ? 2_554 ? 13 AC2 9 HOH G . ? HOH A 442 . ? 4_445 ? 14 AC2 9 DG B 1 ? DG B 11 . ? 2_554 ? 15 AC2 9 DC B 8 ? DC B 18 . ? 1_555 ? 16 AC2 9 DG B 9 ? DG B 19 . ? 1_555 ? 17 AC2 9 DC B 10 ? DC B 20 . ? 1_555 ? 18 AC2 9 HOH H . ? HOH B 362 . ? 1_555 ? 19 AC2 9 HOH H . ? HOH B 367 . ? 1_555 ? 20 AC2 9 HOH H . ? HOH B 449 . ? 2_454 ? 21 AC3 6 HOH G . ? HOH A 302 . ? 1_555 ? 22 AC3 6 HOH G . ? HOH A 305 . ? 1_555 ? 23 AC3 6 HOH G . ? HOH A 306 . ? 1_555 ? 24 AC3 6 HOH G . ? HOH A 307 . ? 1_555 ? 25 AC3 6 HOH H . ? HOH B 303 . ? 1_555 ? 26 AC3 6 HOH H . ? HOH B 304 . ? 1_555 ? 27 AC4 6 HOH H . ? HOH B 1302 . ? 1_555 ? 28 AC4 6 HOH H . ? HOH B 1303 . ? 1_555 ? 29 AC4 6 HOH H . ? HOH B 1304 . ? 1_555 ? 30 AC4 6 HOH H . ? HOH B 1305 . ? 1_555 ? 31 AC4 6 HOH H . ? HOH B 1306 . ? 1_555 ? 32 AC4 6 HOH H . ? HOH B 1307 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A DG 1 ? ? "C1'" A DG 1 ? ? 1.451 1.518 -0.067 0.010 N 2 1 "C2'" A DG 3 ? ? "C1'" A DG 3 ? ? 1.410 1.518 -0.108 0.010 N 3 1 "C2'" A DT 4 ? ? "C1'" A DT 4 ? ? 1.455 1.518 -0.063 0.010 N 4 1 "C2'" B DC 12 ? ? "C1'" B DC 12 ? ? 1.452 1.518 -0.066 0.010 N 5 1 "C2'" B DG 19 ? B "C1'" B DG 19 ? B 1.432 1.518 -0.086 0.010 N 6 1 "O4'" B DG 19 ? A "C1'" B DG 19 ? A 1.519 1.420 0.099 0.011 N 7 1 "O4'" B DG 19 ? B "C1'" B DG 19 ? B 1.520 1.420 0.100 0.011 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? "C2'" A DG 3 ? ? 112.53 106.80 5.73 0.50 N 2 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 101.74 108.00 -6.26 0.70 N 3 1 "O4'" A DA 7 ? A "C1'" A DA 7 ? A N9 A DA 7 ? ? 111.07 108.30 2.77 0.30 N 4 1 "O4'" A DC 8 ? A "C4'" A DC 8 ? A "C3'" A DC 8 ? A 101.02 104.50 -3.48 0.40 N 5 1 "O4'" A DC 8 ? B "C1'" A DC 8 ? B N1 A DC 8 ? ? 111.64 108.30 3.34 0.30 N 6 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? "C2'" B DG 11 ? ? 110.87 106.80 4.07 0.50 N 7 1 "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? "C2'" B DG 13 ? ? 97.90 102.20 -4.30 0.70 N 8 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 112.09 108.30 3.79 0.30 N 9 1 "O4'" B DC 18 ? A "C1'" B DC 18 ? A N1 B DC 18 ? ? 111.08 108.30 2.78 0.30 N 10 1 P B DG 19 ? B "O5'" B DG 19 ? B "C5'" B DG 19 ? B 132.00 120.90 11.10 1.60 N 11 1 "C5'" B DG 19 ? B "C4'" B DG 19 ? B "O4'" B DG 19 ? B 117.16 109.80 7.36 1.10 N 12 1 "C1'" B DG 19 ? A "O4'" B DG 19 ? A "C4'" B DG 19 ? A 101.88 110.10 -8.22 1.00 N 13 1 "C1'" B DG 19 ? B "O4'" B DG 19 ? B "C4'" B DG 19 ? B 102.85 110.10 -7.25 1.00 N 14 1 "O4'" B DG 19 ? A "C1'" B DG 19 ? A "C2'" B DG 19 ? A 113.55 106.80 6.75 0.50 N 15 1 "O4'" B DG 19 ? B "C1'" B DG 19 ? B "C2'" B DG 19 ? B 113.12 106.80 6.32 0.50 N 16 1 "O4'" B DG 19 ? B "C1'" B DG 19 ? B N9 B DG 19 ? ? 99.42 108.00 -8.58 0.70 N 17 1 C8 B DG 19 ? ? N9 B DG 19 ? ? "C1'" B DG 19 ? B 135.84 127.00 8.84 1.30 N 18 1 C4 B DG 19 ? ? N9 B DG 19 ? ? "C1'" B DG 19 ? B 117.95 126.50 -8.55 1.30 N # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MG MG MG N N 147 SPM N1 N N N 148 SPM C2 C N N 149 SPM C3 C N N 150 SPM C4 C N N 151 SPM N5 N N N 152 SPM C6 C N N 153 SPM C7 C N N 154 SPM C8 C N N 155 SPM C9 C N N 156 SPM N10 N N N 157 SPM C11 C N N 158 SPM C12 C N N 159 SPM C13 C N N 160 SPM N14 N N N 161 SPM HN11 H N N 162 SPM HN12 H N N 163 SPM H21 H N N 164 SPM H22 H N N 165 SPM H31 H N N 166 SPM H32 H N N 167 SPM H41 H N N 168 SPM H42 H N N 169 SPM HN5 H N N 170 SPM H61 H N N 171 SPM H62 H N N 172 SPM H71 H N N 173 SPM H72 H N N 174 SPM H81 H N N 175 SPM H82 H N N 176 SPM H91 H N N 177 SPM H92 H N N 178 SPM HN0 H N N 179 SPM H111 H N N 180 SPM H112 H N N 181 SPM H121 H N N 182 SPM H122 H N N 183 SPM H131 H N N 184 SPM H132 H N N 185 SPM HN41 H N N 186 SPM HN42 H N N 187 T23 P P N N 188 T23 OP1 O N N 189 T23 OP2 O N N 190 T23 OP3 O N N 191 T23 "O5'" O N N 192 T23 N1 N N N 193 T23 C6 C N N 194 T23 C2 C N N 195 T23 O2 O N N 196 T23 N3 N N N 197 T23 C4 C N N 198 T23 O4 O N N 199 T23 C5 C N N 200 T23 C5M C N N 201 T23 "C2'" C N R 202 T23 "O2'" O N N 203 T23 C2M C N N 204 T23 "C5'" C N N 205 T23 "C4'" C N S 206 T23 "O4'" O N N 207 T23 "C1'" C N R 208 T23 "C3'" C N R 209 T23 C3M C N N 210 T23 HOP2 H N N 211 T23 HOP3 H N N 212 T23 H6 H N N 213 T23 H3 H N N 214 T23 H5A1 H N N 215 T23 H5A2 H N N 216 T23 H5A3 H N N 217 T23 "H2'" H N N 218 T23 H2M1 H N N 219 T23 H2M2 H N N 220 T23 H2M3 H N N 221 T23 "H5'" H N N 222 T23 "H5''" H N N 223 T23 "H4'" H N N 224 T23 "H1'" H N N 225 T23 "H3'" H N N 226 T23 H3M1 H N N 227 T23 H3M2 H N N 228 T23 H3M3 H N N 229 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 SPM N1 C2 sing N N 152 SPM N1 HN11 sing N N 153 SPM N1 HN12 sing N N 154 SPM C2 C3 sing N N 155 SPM C2 H21 sing N N 156 SPM C2 H22 sing N N 157 SPM C3 C4 sing N N 158 SPM C3 H31 sing N N 159 SPM C3 H32 sing N N 160 SPM C4 N5 sing N N 161 SPM C4 H41 sing N N 162 SPM C4 H42 sing N N 163 SPM N5 C6 sing N N 164 SPM N5 HN5 sing N N 165 SPM C6 C7 sing N N 166 SPM C6 H61 sing N N 167 SPM C6 H62 sing N N 168 SPM C7 C8 sing N N 169 SPM C7 H71 sing N N 170 SPM C7 H72 sing N N 171 SPM C8 C9 sing N N 172 SPM C8 H81 sing N N 173 SPM C8 H82 sing N N 174 SPM C9 N10 sing N N 175 SPM C9 H91 sing N N 176 SPM C9 H92 sing N N 177 SPM N10 C11 sing N N 178 SPM N10 HN0 sing N N 179 SPM C11 C12 sing N N 180 SPM C11 H111 sing N N 181 SPM C11 H112 sing N N 182 SPM C12 C13 sing N N 183 SPM C12 H121 sing N N 184 SPM C12 H122 sing N N 185 SPM C13 N14 sing N N 186 SPM C13 H131 sing N N 187 SPM C13 H132 sing N N 188 SPM N14 HN41 sing N N 189 SPM N14 HN42 sing N N 190 T23 P OP1 doub N N 191 T23 P OP2 sing N N 192 T23 P OP3 sing N N 193 T23 P "O5'" sing N N 194 T23 OP2 HOP2 sing N N 195 T23 OP3 HOP3 sing N N 196 T23 "O5'" "C5'" sing N N 197 T23 N1 C6 sing N N 198 T23 N1 C2 sing N N 199 T23 N1 "C1'" sing N N 200 T23 C6 C5 doub N N 201 T23 C6 H6 sing N N 202 T23 C2 O2 doub N N 203 T23 C2 N3 sing N N 204 T23 N3 C4 sing N N 205 T23 N3 H3 sing N N 206 T23 C4 O4 doub N N 207 T23 C4 C5 sing N N 208 T23 C5 C5M sing N N 209 T23 C5M H5A1 sing N N 210 T23 C5M H5A2 sing N N 211 T23 C5M H5A3 sing N N 212 T23 "C2'" "O2'" sing N N 213 T23 "C2'" "C1'" sing N N 214 T23 "C2'" "C3'" sing N N 215 T23 "C2'" "H2'" sing N N 216 T23 "O2'" C2M sing N N 217 T23 C2M H2M1 sing N N 218 T23 C2M H2M2 sing N N 219 T23 C2M H2M3 sing N N 220 T23 "C5'" "C4'" sing N N 221 T23 "C5'" "H5'" sing N N 222 T23 "C5'" "H5''" sing N N 223 T23 "C4'" "O4'" sing N N 224 T23 "C4'" "C3'" sing N N 225 T23 "C4'" "H4'" sing N N 226 T23 "O4'" "C1'" sing N N 227 T23 "C1'" "H1'" sing N N 228 T23 "C3'" C3M sing N N 229 T23 "C3'" "H3'" sing N N 230 T23 C3M H3M1 sing N N 231 T23 C3M H3M2 sing N N 232 T23 C3M H3M3 sing N N 233 # _ndb_struct_conf_na.entry_id 1DPL _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B DC 10 1_555 -0.273 -0.095 0.206 4.653 -5.473 -1.107 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.124 -0.119 0.081 6.076 -15.519 -0.331 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.343 -0.160 0.171 -3.752 -14.059 -1.163 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.109 -0.135 -0.026 -2.283 -18.917 -0.463 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B T23 6 1_555 0.103 -0.095 0.094 -5.840 -15.506 -3.925 5 A_DA5:T2316_B A 5 ? B 16 ? 20 1 1 A T23 6 1_555 B DA 5 1_555 -0.012 -0.032 0.287 2.445 -12.370 7.592 6 A_T236:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.030 -0.115 0.021 8.205 -6.173 3.974 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.157 -0.131 -0.246 9.764 -8.745 -0.822 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.231 -0.143 -0.217 -10.463 -8.326 0.130 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.206 -0.102 0.106 -3.328 4.693 -0.404 10 A_DC10:DG11_B A 10 ? B 11 ? 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 DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.184 -1.396 3.268 1.972 -1.205 39.979 -1.899 -0.042 3.312 -1.760 -2.882 40.043 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.212 -2.112 3.316 -0.516 10.572 25.847 -6.626 -0.549 2.286 22.472 1.096 27.896 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -0.956 -1.381 3.128 -1.463 6.646 37.342 -2.912 1.298 2.883 10.276 2.263 37.935 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B T23 6 1_555 0.606 -1.444 3.219 1.867 21.046 27.799 -5.154 -0.770 1.762 37.677 -3.343 34.791 4 AA_DT4DA5:T2316DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B T23 6 1_555 A T23 6 1_555 B DA 5 1_555 0.978 -1.192 3.075 0.429 5.816 33.983 -2.836 -1.590 2.850 9.861 -0.728 34.465 5 AA_DA5T236:DA15T2316_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A T23 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.182 -1.406 2.993 -0.811 14.488 30.968 -4.295 0.203 2.146 25.455 1.426 34.123 6 AA_T236DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.180 -2.341 3.322 0.478 4.355 26.498 -6.115 0.505 2.903 9.418 -1.033 26.852 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.480 -2.107 3.735 -0.566 10.801 29.744 -5.938 0.773 2.824 20.218 1.060 31.608 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.183 -1.780 3.253 -0.360 -0.200 34.755 -2.950 -0.362 3.260 -0.334 0.603 34.757 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 1DPL _atom_sites.fract_transf_matrix[1][1] 0.040606 _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] 0.023410 _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] 0.021319 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG N O P # loop_