data_7EDT # _entry.id 7EDT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7EDT pdb_00007edt 10.2210/pdb7edt/pdb WWPDB D_1300021243 ? ? # 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 2022-03-23 2 'Structure model' 1 1 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' pdbx_initial_refinement_model # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7EDT _pdbx_database_status.recvd_initial_deposition_date 2021-03-17 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 0000-0002-5682-3685 'Tada, Y.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'RNA duplex containing CC mispairs' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 0000-0002-5682-3685 primary 'Tada, Y.' 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 ;RNA (5'-R(*GP*GP*AP*CP*UP*CP*CP*GP*GP*(5BU)P*CP*C)-3') ; 3882.208 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 4 water nat water 18.015 163 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GGACUCCGG(5BU)CC' _entity_poly.pdbx_seq_one_letter_code_can GGACUCCGGUCC _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 SPERMINE SPM 3 'SODIUM ION' NA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 C n 1 5 U n 1 6 C n 1 7 C n 1 8 G n 1 9 G n 1 10 5BU n 1 11 C n 1 12 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 12 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 U 5 5 5 U U A . n A 1 6 C 6 6 6 C C A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 G 9 9 9 G G A . n A 1 10 5BU 10 10 10 5BU 5BU A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n B 1 1 G 1 13 13 G G B . n B 1 2 G 2 14 14 G G B . n B 1 3 A 3 15 15 A A B . n B 1 4 C 4 16 16 C C B . n B 1 5 U 5 17 17 U U B . n B 1 6 C 6 18 18 C C B . n B 1 7 C 7 19 19 C C B . n B 1 8 G 8 20 20 G G B . n B 1 9 G 9 21 21 G G B . n B 1 10 5BU 10 22 22 5BU 5BU B . n B 1 11 C 11 23 23 C C B . n B 1 12 C 12 24 24 C 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 SPM 1 401 401 SPM SPM A . D 3 NA 1 402 1 NA NA A . E 4 HOH 1 501 336 HOH HOH A . E 4 HOH 2 502 202 HOH HOH A . E 4 HOH 3 503 227 HOH HOH A . E 4 HOH 4 504 269 HOH HOH A . E 4 HOH 5 505 127 HOH HOH A . E 4 HOH 6 506 273 HOH HOH A . E 4 HOH 7 507 157 HOH HOH A . E 4 HOH 8 508 165 HOH HOH A . E 4 HOH 9 509 197 HOH HOH A . E 4 HOH 10 510 200 HOH HOH A . E 4 HOH 11 511 188 HOH HOH A . E 4 HOH 12 512 159 HOH HOH A . E 4 HOH 13 513 106 HOH HOH A . E 4 HOH 14 514 109 HOH HOH A . E 4 HOH 15 515 120 HOH HOH A . E 4 HOH 16 516 115 HOH HOH A . E 4 HOH 17 517 233 HOH HOH A . E 4 HOH 18 518 125 HOH HOH A . E 4 HOH 19 519 163 HOH HOH A . E 4 HOH 20 520 128 HOH HOH A . E 4 HOH 21 521 103 HOH HOH A . E 4 HOH 22 522 146 HOH HOH A . E 4 HOH 23 523 258 HOH HOH A . E 4 HOH 24 524 231 HOH HOH A . E 4 HOH 25 525 250 HOH HOH A . E 4 HOH 26 526 153 HOH HOH A . E 4 HOH 27 527 122 HOH HOH A . E 4 HOH 28 528 123 HOH HOH A . E 4 HOH 29 529 190 HOH HOH A . E 4 HOH 30 530 105 HOH HOH A . E 4 HOH 31 531 256 HOH HOH A . E 4 HOH 32 532 175 HOH HOH A . E 4 HOH 33 533 230 HOH HOH A . E 4 HOH 34 534 140 HOH HOH A . E 4 HOH 35 535 143 HOH HOH A . E 4 HOH 36 536 116 HOH HOH A . E 4 HOH 37 537 102 HOH HOH A . E 4 HOH 38 538 131 HOH HOH A . E 4 HOH 39 539 174 HOH HOH A . E 4 HOH 40 540 214 HOH HOH A . E 4 HOH 41 541 181 HOH HOH A . E 4 HOH 42 542 107 HOH HOH A . E 4 HOH 43 543 178 HOH HOH A . E 4 HOH 44 544 170 HOH HOH A . E 4 HOH 45 545 132 HOH HOH A . E 4 HOH 46 546 111 HOH HOH A . E 4 HOH 47 547 240 HOH HOH A . E 4 HOH 48 548 201 HOH HOH A . E 4 HOH 49 549 150 HOH HOH A . E 4 HOH 50 550 162 HOH HOH A . E 4 HOH 51 551 168 HOH HOH A . E 4 HOH 52 552 110 HOH HOH A . E 4 HOH 53 553 161 HOH HOH A . E 4 HOH 54 554 169 HOH HOH A . E 4 HOH 55 555 272 HOH HOH A . E 4 HOH 56 556 180 HOH HOH A . E 4 HOH 57 557 172 HOH HOH A . E 4 HOH 58 558 193 HOH HOH A . E 4 HOH 59 559 267 HOH HOH A . E 4 HOH 60 560 192 HOH HOH A . E 4 HOH 61 561 289 HOH HOH A . E 4 HOH 62 562 237 HOH HOH A . E 4 HOH 63 563 290 HOH HOH A . E 4 HOH 64 564 114 HOH HOH A . E 4 HOH 65 565 158 HOH HOH A . E 4 HOH 66 566 204 HOH HOH A . E 4 HOH 67 567 210 HOH HOH A . E 4 HOH 68 568 212 HOH HOH A . E 4 HOH 69 569 321 HOH HOH A . E 4 HOH 70 570 314 HOH HOH A . E 4 HOH 71 571 217 HOH HOH A . E 4 HOH 72 572 263 HOH HOH A . E 4 HOH 73 573 270 HOH HOH A . E 4 HOH 74 574 322 HOH HOH A . E 4 HOH 75 575 326 HOH HOH A . E 4 HOH 76 576 313 HOH HOH A . E 4 HOH 77 577 293 HOH HOH A . F 4 HOH 1 101 185 HOH HOH B . F 4 HOH 2 102 337 HOH HOH B . F 4 HOH 3 103 275 HOH HOH B . F 4 HOH 4 104 189 HOH HOH B . F 4 HOH 5 105 309 HOH HOH B . F 4 HOH 6 106 129 HOH HOH B . F 4 HOH 7 107 221 HOH HOH B . F 4 HOH 8 108 134 HOH HOH B . F 4 HOH 9 109 171 HOH HOH B . F 4 HOH 10 110 176 HOH HOH B . F 4 HOH 11 111 155 HOH HOH B . F 4 HOH 12 112 137 HOH HOH B . F 4 HOH 13 113 130 HOH HOH B . F 4 HOH 14 114 135 HOH HOH B . F 4 HOH 15 115 308 HOH HOH B . F 4 HOH 16 116 154 HOH HOH B . F 4 HOH 17 117 118 HOH HOH B . F 4 HOH 18 118 104 HOH HOH B . F 4 HOH 19 119 166 HOH HOH B . F 4 HOH 20 120 160 HOH HOH B . F 4 HOH 21 121 126 HOH HOH B . F 4 HOH 22 122 121 HOH HOH B . F 4 HOH 23 123 198 HOH HOH B . F 4 HOH 24 124 177 HOH HOH B . F 4 HOH 25 125 199 HOH HOH B . F 4 HOH 26 126 297 HOH HOH B . F 4 HOH 27 127 264 HOH HOH B . F 4 HOH 28 128 141 HOH HOH B . F 4 HOH 29 129 164 HOH HOH B . F 4 HOH 30 130 281 HOH HOH B . F 4 HOH 31 131 216 HOH HOH B . F 4 HOH 32 132 151 HOH HOH B . F 4 HOH 33 133 223 HOH HOH B . F 4 HOH 34 134 101 HOH HOH B . F 4 HOH 35 135 124 HOH HOH B . F 4 HOH 36 136 108 HOH HOH B . F 4 HOH 37 137 144 HOH HOH B . F 4 HOH 38 138 156 HOH HOH B . F 4 HOH 39 139 117 HOH HOH B . F 4 HOH 40 140 173 HOH HOH B . F 4 HOH 41 141 196 HOH HOH B . F 4 HOH 42 142 276 HOH HOH B . F 4 HOH 43 143 208 HOH HOH B . F 4 HOH 44 144 139 HOH HOH B . F 4 HOH 45 145 112 HOH HOH B . F 4 HOH 46 146 182 HOH HOH B . F 4 HOH 47 147 136 HOH HOH B . F 4 HOH 48 148 310 HOH HOH B . F 4 HOH 49 149 300 HOH HOH B . F 4 HOH 50 150 213 HOH HOH B . F 4 HOH 51 151 191 HOH HOH B . F 4 HOH 52 152 149 HOH HOH B . F 4 HOH 53 153 119 HOH HOH B . F 4 HOH 54 154 243 HOH HOH B . F 4 HOH 55 155 142 HOH HOH B . F 4 HOH 56 156 259 HOH HOH B . F 4 HOH 57 157 335 HOH HOH B . F 4 HOH 58 158 138 HOH HOH B . F 4 HOH 59 159 277 HOH HOH B . F 4 HOH 60 160 113 HOH HOH B . F 4 HOH 61 161 167 HOH HOH B . F 4 HOH 62 162 133 HOH HOH B . F 4 HOH 63 163 247 HOH HOH B . F 4 HOH 64 164 261 HOH HOH B . F 4 HOH 65 165 184 HOH HOH B . F 4 HOH 66 166 187 HOH HOH B . F 4 HOH 67 167 249 HOH HOH B . F 4 HOH 68 168 179 HOH HOH B . F 4 HOH 69 169 148 HOH HOH B . F 4 HOH 70 170 205 HOH HOH B . F 4 HOH 71 171 268 HOH HOH B . F 4 HOH 72 172 152 HOH HOH B . F 4 HOH 73 173 209 HOH HOH B . F 4 HOH 74 174 266 HOH HOH B . F 4 HOH 75 175 257 HOH HOH B . F 4 HOH 76 176 278 HOH HOH B . F 4 HOH 77 177 262 HOH HOH B . F 4 HOH 78 178 242 HOH HOH B . F 4 HOH 79 179 234 HOH HOH B . F 4 HOH 80 180 145 HOH HOH B . F 4 HOH 81 181 255 HOH HOH B . F 4 HOH 82 182 282 HOH HOH B . F 4 HOH 83 183 238 HOH HOH B . F 4 HOH 84 184 226 HOH HOH B . F 4 HOH 85 185 316 HOH HOH B . F 4 HOH 86 186 294 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 A SPM 401 ? N1 ? C SPM 1 N1 2 1 N 1 A SPM 401 ? C2 ? C SPM 1 C2 3 1 N 1 A SPM 401 ? C3 ? C SPM 1 C3 # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? d*TREK ? ? ? 9.4SSI 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? d*TREK ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 # _cell.angle_alpha 93.850 _cell.angle_alpha_esd ? _cell.angle_beta 106.020 _cell.angle_beta_esd ? _cell.angle_gamma 103.210 _cell.angle_gamma_esd ? _cell.entry_id 7EDT _cell.details ? _cell.formula_units_Z ? _cell.length_a 24.296 _cell.length_a_esd ? _cell.length_b 24.852 _cell.length_b_esd ? _cell.length_c 28.249 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 2 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EDT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7EDT _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.04 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 39.58 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'sodium cacodylate, MPD, spermine tetrahydrochloride' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-06-06 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9204 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'PHOTON FACTORY BEAMLINE AR-NE3A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9204 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline AR-NE3A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 7EDT _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.200 _reflns.d_resolution_low 19.270 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 17973 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 93.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.850 _reflns.pdbx_Rmerge_I_obs 0.079 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 10.000 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 0.940 _reflns.pdbx_scaling_rejects 524 _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.079 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 69661 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split 1.200 1.240 ? 3.600 6621 ? ? ? 1766 92.300 ? ? ? ? 0.261 ? ? ? ? ? ? ? ? 3.750 ? 0.820 ? ? ? ? ? 1 1 ? ? ? 1.240 1.290 ? 3.800 6966 ? ? ? 1786 92.800 ? ? ? ? 0.252 ? ? ? ? ? ? ? ? 3.900 ? 0.800 ? ? ? ? 8 2 1 ? ? ? 1.290 1.350 ? 4.100 7035 ? ? ? 1799 93.500 ? ? ? ? 0.228 ? ? ? ? ? ? ? ? 3.910 ? 0.790 ? ? ? ? ? 3 1 ? ? ? 1.350 1.420 ? 4.600 7015 ? ? ? 1796 93.800 ? ? ? ? 0.199 ? ? ? ? ? ? ? ? 3.900 ? 0.730 ? ? ? ? 3 4 1 ? ? ? 1.420 1.510 ? 5.200 7047 ? ? ? 1814 94.500 ? ? ? ? 0.166 ? ? ? ? ? ? ? ? 3.880 ? 0.730 ? ? ? ? 9 5 1 ? ? ? 1.510 1.630 ? 6.800 7096 ? ? ? 1812 94.900 ? ? ? ? 0.122 ? ? ? ? ? ? ? ? 3.910 ? 0.710 ? ? ? ? 13 6 1 ? ? ? 1.630 1.790 ? 10.100 7167 ? ? ? 1823 95.300 ? ? ? ? 0.091 ? ? ? ? ? ? ? ? 3.910 ? 0.750 ? ? ? ? 38 7 1 ? ? ? 1.790 2.050 ? 14.200 7203 ? ? ? 1842 95.700 ? ? ? ? 0.070 ? ? ? ? ? ? ? ? 3.860 ? 0.870 ? ? ? ? 91 8 1 ? ? ? 2.050 2.580 ? 22.200 7141 ? ? ? 1830 95.900 ? ? ? ? 0.055 ? ? ? ? ? ? ? ? 3.820 ? 1.260 ? ? ? ? 154 9 1 ? ? ? 2.580 19.270 ? 27.600 6370 ? ? ? 1705 89.100 ? ? ? ? 0.061 ? ? ? ? ? ? ? ? 3.610 ? 2.120 ? ? ? ? 208 10 1 ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 64.900 _refine.B_iso_mean 15.9171 _refine.B_iso_min 8.350 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 7EDT _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.2000 _refine.ls_d_res_low 19.2700 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 17949 _refine.ls_number_reflns_R_free 1840 _refine.ls_number_reflns_R_work 16109 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 93.6400 _refine.ls_percent_reflns_R_free 10.2500 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1471 _refine.ls_R_factor_R_free 0.1767 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1439 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'RNA duplex constructed using Coot' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 15.7300 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.1000 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.2000 _refine_hist.d_res_low 19.2700 _refine_hist.number_atoms_solvent 163 _refine_hist.number_atoms_total 679 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_ligand 21.65 _refine_hist.pdbx_B_iso_mean_solvent 28.66 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 504 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 1.2000 1.2300 1371 . 153 1218 92.0000 . . . 0.1953 0.0000 0.1549 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.2300 1.2700 1357 . 142 1215 92.0000 . . . 0.1970 0.0000 0.1416 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.2700 1.3100 1364 . 145 1219 93.0000 . . . 0.2101 0.0000 0.1576 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.3100 1.3600 1392 . 137 1255 94.0000 . . . 0.1862 0.0000 0.1372 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.3600 1.4100 1361 . 133 1228 93.0000 . . . 0.1739 0.0000 0.1429 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.4100 1.4700 1384 . 150 1234 95.0000 . . . 0.1797 0.0000 0.1444 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.4700 1.5500 1402 . 138 1264 94.0000 . . . 0.1849 0.0000 0.1411 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.5500 1.6500 1384 . 127 1257 95.0000 . . . 0.1676 0.0000 0.1270 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.6500 1.7800 1426 . 158 1268 96.0000 . . . 0.1473 0.0000 0.1220 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.7800 1.9600 1391 . 156 1235 95.0000 . . . 0.1771 0.0000 0.1391 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 1.9600 2.2400 1408 . 140 1268 95.0000 . . . 0.1644 0.0000 0.1408 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 2.2400 2.8200 1427 . 131 1296 97.0000 . . . 0.1922 0.0000 0.1611 . . . . . . . 13 . . . 'X-RAY DIFFRACTION' 2.8200 19.2700 1282 . 130 1152 87.0000 . . . 0.1760 0.0000 0.1478 . . . . . . . 13 . . . # _struct.entry_id 7EDT _struct.title 'RNA duplex containing CC mispairs' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7EDT _struct_keywords.text 'Mismatch, base pair, RNA' _struct_keywords.pdbx_keywords RNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7EDT _struct_ref.pdbx_db_accession 7EDT _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7EDT A 1 ? 12 ? 7EDT 1 ? 12 ? 1 12 2 1 7EDT B 1 ? 12 ? 7EDT 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2930 ? 1 MORE -16 ? 1 'SSA (A^2)' 4180 ? # _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 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 9 "O3'" ? ? ? 1_555 A 5BU 10 P ? ? A G 9 A 5BU 10 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A 5BU 10 "O3'" ? ? ? 1_555 A C 11 P ? ? A 5BU 10 A C 11 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale both ? B G 9 "O3'" ? ? ? 1_555 B 5BU 10 P ? ? B G 21 B 5BU 22 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B 5BU 10 "O3'" ? ? ? 1_555 B C 11 P ? ? B 5BU 22 B C 23 1_555 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? A C 6 "O2'" ? ? ? 1_555 D NA . NA ? ? A C 6 A NA 402 1_555 ? ? ? ? ? ? ? 2.497 ? ? metalc2 metalc ? ? A C 7 OP2 ? ? ? 1_555 D NA . NA ? ? A C 7 A NA 402 1_555 ? ? ? ? ? ? ? 2.333 ? ? metalc3 metalc ? ? A G 8 O6 ? ? ? 1_555 D NA . NA ? ? A G 8 A NA 402 1_555 ? ? ? ? ? ? ? 2.494 ? ? metalc4 metalc ? ? D NA . NA ? ? ? 1_555 E HOH . O ? ? A NA 402 A HOH 537 1_555 ? ? ? ? ? ? ? 2.392 ? ? metalc5 metalc ? ? D NA . NA ? ? ? 1_555 F HOH . O ? ? A NA 402 B HOH 134 1_555 ? ? ? ? ? ? ? 2.431 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B 5BU 10 N3 ? ? A A 3 B 5BU 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B 5BU 10 O4 ? ? A A 3 B 5BU 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 4 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 4 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 4 B G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 5 N3 ? ? ? 1_555 B G 8 O6 ? ? A U 5 B G 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog13 hydrog ? ? A U 5 O2 ? ? ? 1_555 B G 8 N1 ? ? A U 5 B G 20 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 B C 7 N4 ? ? A C 6 B C 19 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 B C 6 O2 ? ? A C 7 B C 18 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 B U 5 O2 ? ? A G 8 B U 17 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A G 8 O6 ? ? ? 1_555 B U 5 N3 ? ? A G 8 B U 17 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog18 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 9 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 9 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 9 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 5BU 10 N3 ? ? ? 1_555 B A 3 N1 ? ? A 5BU 10 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 5BU 10 O4 ? ? ? 1_555 B A 3 N6 ? ? A 5BU 10 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 12 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 12 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 12 B G 13 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 "O2'" ? A C 6 ? A C 6 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 OP2 ? A C 7 ? A C 7 ? 1_555 94.2 ? 2 "O2'" ? A C 6 ? A C 6 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O6 ? A G 8 ? A G 8 ? 1_555 90.4 ? 3 OP2 ? A C 7 ? A C 7 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O6 ? A G 8 ? A G 8 ? 1_555 167.7 ? 4 "O2'" ? A C 6 ? A C 6 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? E HOH . ? A HOH 537 ? 1_555 171.0 ? 5 OP2 ? A C 7 ? A C 7 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? E HOH . ? A HOH 537 ? 1_555 94.7 ? 6 O6 ? A G 8 ? A G 8 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? E HOH . ? A HOH 537 ? 1_555 81.2 ? 7 "O2'" ? A C 6 ? A C 6 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? F HOH . ? B HOH 134 ? 1_555 80.5 ? 8 OP2 ? A C 7 ? A C 7 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? F HOH . ? B HOH 134 ? 1_555 105.0 ? 9 O6 ? A G 8 ? A G 8 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? F HOH . ? B HOH 134 ? 1_555 87.0 ? 10 O ? E HOH . ? A HOH 537 ? 1_555 NA ? D NA . ? A NA 402 ? 1_555 O ? F HOH . ? B HOH 134 ? 1_555 95.6 ? # _pdbx_entry_details.entry_id 7EDT _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 NA NA NA N N 148 SPM N1 N N N 149 SPM C2 C N N 150 SPM C3 C N N 151 SPM C4 C N N 152 SPM N5 N N N 153 SPM C6 C N N 154 SPM C7 C N N 155 SPM C8 C N N 156 SPM C9 C N N 157 SPM N10 N N N 158 SPM C11 C N N 159 SPM C12 C N N 160 SPM C13 C N N 161 SPM N14 N N N 162 SPM HN11 H N N 163 SPM HN12 H N N 164 SPM H21 H N N 165 SPM H22 H N N 166 SPM H31 H N N 167 SPM H32 H N N 168 SPM H41 H N N 169 SPM H42 H N N 170 SPM HN5 H N N 171 SPM H61 H N N 172 SPM H62 H N N 173 SPM H71 H N N 174 SPM H72 H N N 175 SPM H81 H N N 176 SPM H82 H N N 177 SPM H91 H N N 178 SPM H92 H N N 179 SPM HN0 H N N 180 SPM H111 H N N 181 SPM H112 H N N 182 SPM H121 H N N 183 SPM H122 H N N 184 SPM H131 H N N 185 SPM H132 H N N 186 SPM HN41 H N N 187 SPM HN42 H N N 188 U OP3 O N N 189 U P P N N 190 U OP1 O N N 191 U OP2 O N N 192 U "O5'" O N N 193 U "C5'" C N N 194 U "C4'" C N R 195 U "O4'" O N N 196 U "C3'" C N S 197 U "O3'" O N N 198 U "C2'" C N R 199 U "O2'" O N N 200 U "C1'" C N R 201 U N1 N N N 202 U C2 C N N 203 U O2 O N N 204 U N3 N N N 205 U C4 C N N 206 U O4 O N N 207 U C5 C N N 208 U C6 C N N 209 U HOP3 H N N 210 U HOP2 H N N 211 U "H5'" H N N 212 U "H5''" H N N 213 U "H4'" H N N 214 U "H3'" H N N 215 U "HO3'" H N N 216 U "H2'" H N N 217 U "HO2'" H N N 218 U "H1'" H N N 219 U H3 H N N 220 U H5 H N N 221 U H6 H N N 222 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 SPM N1 C2 sing N N 153 SPM N1 HN11 sing N N 154 SPM N1 HN12 sing N N 155 SPM C2 C3 sing N N 156 SPM C2 H21 sing N N 157 SPM C2 H22 sing N N 158 SPM C3 C4 sing N N 159 SPM C3 H31 sing N N 160 SPM C3 H32 sing N N 161 SPM C4 N5 sing N N 162 SPM C4 H41 sing N N 163 SPM C4 H42 sing N N 164 SPM N5 C6 sing N N 165 SPM N5 HN5 sing N N 166 SPM C6 C7 sing N N 167 SPM C6 H61 sing N N 168 SPM C6 H62 sing N N 169 SPM C7 C8 sing N N 170 SPM C7 H71 sing N N 171 SPM C7 H72 sing N N 172 SPM C8 C9 sing N N 173 SPM C8 H81 sing N N 174 SPM C8 H82 sing N N 175 SPM C9 N10 sing N N 176 SPM C9 H91 sing N N 177 SPM C9 H92 sing N N 178 SPM N10 C11 sing N N 179 SPM N10 HN0 sing N N 180 SPM C11 C12 sing N N 181 SPM C11 H111 sing N N 182 SPM C11 H112 sing N N 183 SPM C12 C13 sing N N 184 SPM C12 H121 sing N N 185 SPM C12 H122 sing N N 186 SPM C13 N14 sing N N 187 SPM C13 H131 sing N N 188 SPM C13 H132 sing N N 189 SPM N14 HN41 sing N N 190 SPM N14 HN42 sing N N 191 U OP3 P sing N N 192 U OP3 HOP3 sing N N 193 U P OP1 doub N N 194 U P OP2 sing N N 195 U P "O5'" sing N N 196 U OP2 HOP2 sing N N 197 U "O5'" "C5'" sing N N 198 U "C5'" "C4'" sing N N 199 U "C5'" "H5'" sing N N 200 U "C5'" "H5''" sing N N 201 U "C4'" "O4'" sing N N 202 U "C4'" "C3'" sing N N 203 U "C4'" "H4'" sing N N 204 U "O4'" "C1'" sing N N 205 U "C3'" "O3'" sing N N 206 U "C3'" "C2'" sing N N 207 U "C3'" "H3'" sing N N 208 U "O3'" "HO3'" sing N N 209 U "C2'" "O2'" sing N N 210 U "C2'" "C1'" sing N N 211 U "C2'" "H2'" sing N N 212 U "O2'" "HO2'" sing N N 213 U "C1'" N1 sing N N 214 U "C1'" "H1'" sing N N 215 U N1 C2 sing N N 216 U N1 C6 sing N N 217 U C2 O2 doub N N 218 U C2 N3 sing N N 219 U N3 C4 sing N N 220 U N3 H3 sing N N 221 U C4 O4 doub N N 222 U C4 C5 sing N N 223 U C5 C6 doub N N 224 U C5 H5 sing N N 225 U C6 H6 sing N N 226 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7EDT 'double helix' 7EDT '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 G 1 1_555 B C 12 1_555 -0.143 -0.059 0.116 -8.441 -9.748 0.582 1 A_G1:C24_B A 1 ? B 24 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.265 -0.130 0.134 -4.140 -8.611 0.039 2 A_G2:C23_B A 2 ? B 23 ? 19 1 1 A A 3 1_555 B 5BU 10 1_555 0.089 -0.130 -0.033 -0.255 -12.959 1.348 3 A_A3:5BU22_B A 3 ? B 22 ? 20 1 1 A C 4 1_555 B G 9 1_555 0.300 -0.122 0.150 -0.014 -15.321 2.239 4 A_C4:G21_B A 4 ? B 21 ? 19 1 1 A U 5 1_555 B G 8 1_555 2.488 -0.574 0.013 -8.647 -12.587 -2.270 5 A_U5:G20_B A 5 ? B 20 ? 28 1 1 A C 6 1_555 B C 7 1_555 5.077 -2.353 0.817 20.722 28.139 -82.001 6 A_C6:C19_B A 6 ? B 19 ? ? 4 1 A C 7 1_555 B C 6 1_555 -6.403 -4.959 -0.822 16.145 -28.447 -40.224 7 A_C7:C18_B A 7 ? B 18 ? ? 4 1 A G 8 1_555 B U 5 1_555 -2.393 -0.619 -0.229 -6.144 -12.650 1.263 8 A_G8:U17_B A 8 ? B 17 ? 28 1 1 A G 9 1_555 B C 4 1_555 -0.256 -0.124 -0.047 -9.768 -9.031 1.117 9 A_G9:C16_B A 9 ? B 16 ? 19 1 1 A 5BU 10 1_555 B A 3 1_555 -0.107 -0.141 0.002 -3.377 -11.938 0.025 10 A_5BU10:A15_B A 10 ? B 15 ? 20 1 1 A C 11 1_555 B G 2 1_555 0.279 -0.166 -0.023 1.749 -8.733 -1.043 11 A_C11:G14_B A 11 ? B 14 ? 19 1 1 A C 12 1_555 B G 1 1_555 0.210 -0.111 0.039 3.312 -10.201 -0.188 12 A_C12:G13_B A 12 ? B 13 ? 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 G 1 1_555 B C 12 1_555 A G 2 1_555 B C 11 1_555 -0.629 -1.582 3.094 -1.510 3.914 35.526 -3.097 0.823 2.932 6.388 2.465 35.765 1 AA_G1G2:C23C24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A G 2 1_555 B C 11 1_555 A A 3 1_555 B 5BU 10 1_555 0.805 -1.851 3.115 3.931 7.648 26.880 -5.394 -0.833 2.590 15.942 -8.194 28.198 2 AA_G2A3:5BU22C23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A A 3 1_555 B 5BU 10 1_555 A C 4 1_555 B G 9 1_555 0.430 -1.812 3.226 0.335 0.175 35.153 -3.025 -0.663 3.221 0.290 -0.554 35.155 3 AA_A3C4:G215BU22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A C 4 1_555 B G 9 1_555 A U 5 1_555 B G 8 1_555 -0.190 -1.647 3.420 4.874 6.264 40.920 -2.982 0.786 3.104 8.859 -6.893 41.650 4 AA_C4U5:G20G21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A U 5 1_555 B G 8 1_555 A C 6 1_555 B C 7 1_555 -4.736 -2.309 2.986 10.512 8.377 32.584 -4.585 8.796 0.860 14.200 -17.819 35.178 5 AA_U5C6:C19G20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A C 6 1_555 B C 7 1_555 A C 7 1_555 B C 6 1_555 2.271 2.559 3.603 0.498 11.772 -8.885 -17.059 9.149 0.059 -53.060 2.245 -14.748 6 AA_C6C7:C18C19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A C 7 1_555 B C 6 1_555 A G 8 1_555 B U 5 1_555 3.372 -1.443 4.147 -8.536 17.767 58.252 -2.387 -3.777 3.153 17.706 8.506 61.218 7 AA_C7G8:U17C18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A G 8 1_555 B U 5 1_555 A G 9 1_555 B C 4 1_555 -0.030 -1.626 3.315 -2.686 6.205 39.072 -3.107 -0.263 3.027 9.193 3.980 39.630 8 AA_G8G9:C16U17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A G 9 1_555 B C 4 1_555 A 5BU 10 1_555 B A 3 1_555 -0.629 -1.484 3.098 -0.871 3.367 32.156 -3.217 0.986 2.947 6.057 1.567 32.338 9 AA_G95BU10:A15C16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A 5BU 10 1_555 B A 3 1_555 A C 11 1_555 B G 2 1_555 0.091 -1.205 3.124 -0.348 4.194 33.598 -2.700 -0.209 2.955 7.220 0.598 33.853 10 AA_5BU10C11:G14A15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A C 11 1_555 B G 2 1_555 A C 12 1_555 B G 1 1_555 0.848 -1.903 3.142 2.800 4.707 32.298 -4.130 -1.056 2.904 8.387 -4.988 32.747 11 AA_C11C12:G13G14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_audit_support.funding_organization 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 24245037 _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type other _pdbx_initial_refinement_model.source_name ? _pdbx_initial_refinement_model.details 'RNA duplex constructed using Coot' # _atom_sites.entry_id 7EDT _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.041159 _atom_sites.fract_transf_matrix[1][2] 0.009663 _atom_sites.fract_transf_matrix[1][3] 0.013291 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041333 _atom_sites.fract_transf_matrix[2][3] 0.005811 _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] 0.037192 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol BR C N NA O P # loop_