data_4O5Y # _entry.id 4O5Y # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 4O5Y pdb_00004o5y 10.2210/pdb4o5y/pdb NDB NA2871 ? ? RCSB RCSB084083 ? ? WWPDB D_1000084083 ? ? # 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 2014-07-02 2 'Structure model' 1 1 2017-11-22 3 'Structure model' 1 2 2024-03-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' software 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_software.name' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_comp_id' 13 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 14 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_atom_id' 15 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_comp_id' 16 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 17 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 18 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 19 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 20 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 21 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 22 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 23 3 'Structure model' '_pdbx_struct_conn_angle.value' 24 3 'Structure model' '_struct_conn.pdbx_dist_value' 25 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 26 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 27 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 28 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 29 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 30 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 31 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 32 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 33 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 34 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 35 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 36 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 37 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 38 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 39 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 40 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 41 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 4O5Y _pdbx_database_status.status_code REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2013-12-20 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4ITD . unspecified PDB 4IJ0 . unspecified PDB 4O5W . unspecified PDB 4O5X . unspecified PDB 4O5Z . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhang, F.' 1 'Tsunoda, M.' 2 'Suzuki, K.' 3 'Kikuchi, Y.' 4 'Wilkinson, O.' 5 'Millington, C.L.' 6 'Margison, G.P.' 7 'Williams, D.M.' 8 'Takenaka, A.' 9 # _citation.id primary _citation.title 'O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 70 _citation.page_first 1669 _citation.page_last 1679 _citation.year 2014 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24914978 _citation.pdbx_database_id_DOI 10.1107/S1399004714006178 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, F.' 1 ? primary 'Tsunoda, M.' 2 ? primary 'Kikuchi, Y.' 3 ? primary 'Wilkinson, O.' 4 ? primary 'Millington, C.L.' 5 ? primary 'Margison, G.P.' 6 ? primary 'Williams, D.M.' 7 ? primary 'Takenaka, A.' 8 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*CP*(C6G)P*AP*AP*TP*TP*TP*GP*CP*G)-3') ; 3736.439 2 ? ? ? 'damaged DNA' 2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 3 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 4 water nat water 18.015 138 ? ? ? ? # _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 '(DC)(DG)(DC)(C6G)(DA)(DA)(DT)(DT)(DT)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCXAATTTGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 'BARIUM ION' BA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 C6G n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DT n 1 10 DG n 1 11 DC n 1 12 DG 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 BA non-polymer . 'BARIUM ION' ? 'Ba 2' 137.327 C6G 'DNA linking' n '6-(carboxymethoxy)-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-2-amine' ? 'C12 H16 N5 O9 P' 405.257 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 C6G 4 4 4 C6G C6G A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 C6G 4 16 16 C6G C6G B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DT 9 21 21 DT DT B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 K 1 101 1 K K A . D 3 BA 1 101 1 BA BA B . E 4 HOH 1 201 5 HOH HOH A . E 4 HOH 2 202 6 HOH HOH A . E 4 HOH 3 203 8 HOH HOH A . E 4 HOH 4 204 9 HOH HOH A . E 4 HOH 5 205 10 HOH HOH A . E 4 HOH 6 206 11 HOH HOH A . E 4 HOH 7 207 15 HOH HOH A . E 4 HOH 8 208 16 HOH HOH A . E 4 HOH 9 209 17 HOH HOH A . E 4 HOH 10 210 18 HOH HOH A . E 4 HOH 11 211 19 HOH HOH A . E 4 HOH 12 212 22 HOH HOH A . E 4 HOH 13 213 25 HOH HOH A . E 4 HOH 14 214 27 HOH HOH A . E 4 HOH 15 215 32 HOH HOH A . E 4 HOH 16 216 37 HOH HOH A . E 4 HOH 17 217 50 HOH HOH A . E 4 HOH 18 218 58 HOH HOH A . E 4 HOH 19 219 60 HOH HOH A . E 4 HOH 20 220 69 HOH HOH A . E 4 HOH 21 221 75 HOH HOH A . E 4 HOH 22 222 79 HOH HOH A . E 4 HOH 23 223 80 HOH HOH A . E 4 HOH 24 224 81 HOH HOH A . E 4 HOH 25 225 89 HOH HOH A . E 4 HOH 26 226 98 HOH HOH A . E 4 HOH 27 227 109 HOH HOH A . E 4 HOH 28 228 111 HOH HOH A . E 4 HOH 29 229 118 HOH HOH A . E 4 HOH 30 230 122 HOH HOH A . E 4 HOH 31 231 131 HOH HOH A . E 4 HOH 32 232 137 HOH HOH A . E 4 HOH 33 233 144 HOH HOH A . E 4 HOH 34 234 150 HOH HOH A . E 4 HOH 35 235 160 HOH HOH A . E 4 HOH 36 236 162 HOH HOH A . E 4 HOH 37 237 173 HOH HOH A . E 4 HOH 38 238 174 HOH HOH A . E 4 HOH 39 239 179 HOH HOH A . E 4 HOH 40 240 182 HOH HOH A . E 4 HOH 41 241 185 HOH HOH A . E 4 HOH 42 242 189 HOH HOH A . E 4 HOH 43 243 191 HOH HOH A . E 4 HOH 44 244 199 HOH HOH A . E 4 HOH 45 245 232 HOH HOH A . E 4 HOH 46 246 264 HOH HOH A . E 4 HOH 47 247 318 HOH HOH A . E 4 HOH 48 248 328 HOH HOH A . E 4 HOH 49 249 331 HOH HOH A . E 4 HOH 50 250 332 HOH HOH A . E 4 HOH 51 251 340 HOH HOH A . E 4 HOH 52 252 343 HOH HOH A . E 4 HOH 53 253 344 HOH HOH A . E 4 HOH 54 254 345 HOH HOH A . E 4 HOH 55 255 5 HOH HOH A . E 4 HOH 56 256 10 HOH HOH A . E 4 HOH 57 257 15 HOH HOH A . E 4 HOH 58 258 16 HOH HOH A . E 4 HOH 59 259 17 HOH HOH A . E 4 HOH 60 260 24 HOH HOH A . E 4 HOH 61 261 27 HOH HOH A . E 4 HOH 62 262 28 HOH HOH A . E 4 HOH 63 263 29 HOH HOH A . E 4 HOH 64 264 36 HOH HOH A . E 4 HOH 65 265 38 HOH HOH A . E 4 HOH 66 266 40 HOH HOH A . F 4 HOH 1 201 2 HOH HOH B . F 4 HOH 2 202 12 HOH HOH B . F 4 HOH 3 203 13 HOH HOH B . F 4 HOH 4 204 20 HOH HOH B . F 4 HOH 5 205 24 HOH HOH B . F 4 HOH 6 206 28 HOH HOH B . F 4 HOH 7 207 30 HOH HOH B . F 4 HOH 8 208 34 HOH HOH B . F 4 HOH 9 209 35 HOH HOH B . F 4 HOH 10 210 36 HOH HOH B . F 4 HOH 11 211 40 HOH HOH B . F 4 HOH 12 212 43 HOH HOH B . F 4 HOH 13 213 44 HOH HOH B . F 4 HOH 14 214 53 HOH HOH B . F 4 HOH 15 215 54 HOH HOH B . F 4 HOH 16 216 56 HOH HOH B . F 4 HOH 17 217 63 HOH HOH B . F 4 HOH 18 218 64 HOH HOH B . F 4 HOH 19 219 70 HOH HOH B . F 4 HOH 20 220 71 HOH HOH B . F 4 HOH 21 221 73 HOH HOH B . F 4 HOH 22 222 85 HOH HOH B . F 4 HOH 23 223 90 HOH HOH B . F 4 HOH 24 224 93 HOH HOH B . F 4 HOH 25 225 96 HOH HOH B . F 4 HOH 26 226 99 HOH HOH B . F 4 HOH 27 227 100 HOH HOH B . F 4 HOH 28 228 101 HOH HOH B . F 4 HOH 29 229 103 HOH HOH B . F 4 HOH 30 230 120 HOH HOH B . F 4 HOH 31 231 124 HOH HOH B . F 4 HOH 32 232 128 HOH HOH B . F 4 HOH 33 233 129 HOH HOH B . F 4 HOH 34 234 139 HOH HOH B . F 4 HOH 35 235 142 HOH HOH B . F 4 HOH 36 236 143 HOH HOH B . F 4 HOH 37 237 149 HOH HOH B . F 4 HOH 38 238 153 HOH HOH B . F 4 HOH 39 239 171 HOH HOH B . F 4 HOH 40 240 195 HOH HOH B . F 4 HOH 41 241 249 HOH HOH B . F 4 HOH 42 242 263 HOH HOH B . F 4 HOH 43 243 266 HOH HOH B . F 4 HOH 44 244 274 HOH HOH B . F 4 HOH 45 245 275 HOH HOH B . F 4 HOH 46 246 282 HOH HOH B . F 4 HOH 47 247 291 HOH HOH B . F 4 HOH 48 248 306 HOH HOH B . F 4 HOH 49 249 307 HOH HOH B . F 4 HOH 50 250 313 HOH HOH B . F 4 HOH 51 251 315 HOH HOH B . F 4 HOH 52 252 324 HOH HOH B . F 4 HOH 53 253 337 HOH HOH B . F 4 HOH 54 254 339 HOH HOH B . F 4 HOH 55 255 341 HOH HOH B . F 4 HOH 56 256 342 HOH HOH B . F 4 HOH 57 257 1 HOH HOH B . F 4 HOH 58 258 2 HOH HOH B . F 4 HOH 59 259 6 HOH HOH B . F 4 HOH 60 260 7 HOH HOH B . F 4 HOH 61 261 9 HOH HOH B . F 4 HOH 62 262 11 HOH HOH B . F 4 HOH 63 263 12 HOH HOH B . F 4 HOH 64 264 13 HOH HOH B . F 4 HOH 65 265 18 HOH HOH B . F 4 HOH 66 266 19 HOH HOH B . F 4 HOH 67 267 20 HOH HOH B . F 4 HOH 68 268 21 HOH HOH B . F 4 HOH 69 269 25 HOH HOH B . F 4 HOH 70 270 32 HOH HOH B . F 4 HOH 71 271 34 HOH HOH B . F 4 HOH 72 272 39 HOH HOH B . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 MOLREP . ? program 'Alexei Vaguine' alexei@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/molrep.html Fortran_77 ? 3 REFMAC 5.5.0109 ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.14 'Dec. 10, 2013' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 DENZO . ? ? ? ? 'data reduction' ? ? ? # _cell.entry_id 4O5Y _cell.length_a 25.957 _cell.length_b 41.525 _cell.length_c 64.691 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4O5Y _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4O5Y _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.33 _exptl_crystal.density_percent_sol 47.27 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;5%(v/v)MPD, 6mM spermine 4HCL, 40mM KCL, 10mM BaCL2, 20mM Na cacodylate(pH6.0), 0.5mM DNA, vapor diffusion, hanging drop, temperature 277K ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2012-04-21 _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 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-5A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-5A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4O5Y _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.000 _reflns.d_resolution_high 1.750 _reflns.number_obs 7413 _reflns.number_all ? _reflns.percent_possible_obs 98.000 _reflns.pdbx_Rmerge_I_obs 0.081 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.200 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.500 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _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.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared 1 1 1.750 1.780 94.400 0.484 ? ? 10.100 ? ? ? ? ? ? 1 2 1.780 1.810 98.400 0.442 ? ? 11.400 ? ? ? ? ? ? 1 3 1.810 1.850 98.900 0.493 ? ? 13.100 ? ? ? ? ? ? 1 4 1.850 1.890 99.700 0.412 ? ? 13.500 ? ? ? ? ? ? 1 5 1.890 1.930 98.600 0.386 ? ? 13.800 ? ? ? ? ? ? 1 6 1.930 1.970 98.700 0.339 ? ? 13.700 ? ? ? ? ? ? 1 7 1.970 2.020 99.500 0.254 ? ? 13.300 ? ? ? ? ? ? 1 8 2.020 2.070 99.700 0.208 ? ? 13.300 ? ? ? ? ? ? 1 9 2.070 2.140 99.200 0.169 ? ? 13.000 ? ? ? ? ? ? 1 10 2.140 2.200 99.200 0.164 ? ? 12.900 ? ? ? ? ? ? 1 11 2.200 2.280 99.400 0.135 ? ? 12.700 ? ? ? ? ? ? 1 12 2.280 2.380 99.500 0.131 ? ? 12.400 ? ? ? ? ? ? 1 13 2.380 2.480 99.700 0.106 ? ? 12.000 ? ? ? ? ? ? 1 14 2.480 2.610 99.500 0.091 ? ? 11.800 ? ? ? ? ? ? 1 15 2.610 2.780 99.700 0.082 ? ? 11.400 ? ? ? ? ? ? 1 16 2.780 2.990 99.200 0.072 ? ? 10.800 ? ? ? ? ? ? 1 17 2.990 3.290 95.400 0.060 ? ? 9.300 ? ? ? ? ? ? 1 18 3.290 3.770 94.400 0.053 ? ? 7.800 ? ? ? ? ? ? 1 19 3.770 4.750 95.700 0.048 ? ? 7.300 ? ? ? ? ? ? 1 20 4.750 50.000 91.700 0.047 ? ? 6.600 ? ? ? ? ? ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4O5Y _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 7022 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.95 _refine.ls_d_res_high 1.75 _refine.ls_percent_reflns_obs 97.59 _refine.ls_R_factor_obs 0.23066 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.22875 _refine.ls_R_factor_R_free 0.26859 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 339 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 0.500 _refine.occupancy_max 1.000 _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.938 _refine.B_iso_mean 30.986 _refine.aniso_B[1][1] 1.18 _refine.aniso_B[2][2] -0.11 _refine.aniso_B[3][3] -1.07 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.154 _refine.pdbx_overall_ESU_R_Free 0.144 _refine.overall_SU_ML 0.102 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 3.228 _refine.overall_SU_R_Cruickshank_DPI 0.1522 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_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 496 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 138 _refine_hist.number_atoms_total 636 _refine_hist.d_res_high 1.75 _refine_hist.d_res_low 34.95 # 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 r_bond_refined_d 0.024 0.021 ? 552 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.356 3.000 ? 834 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.336 0.200 ? 94 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.023 0.020 ? 262 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.614 3.000 ? 552 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 3.489 4.500 ? 834 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.745 _refine_ls_shell.d_res_low 1.790 _refine_ls_shell.number_reflns_R_work 461 _refine_ls_shell.R_factor_R_work 0.273 _refine_ls_shell.percent_reflns_obs 93.64 _refine_ls_shell.R_factor_R_free 0.219 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 25 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 4O5Y _struct.title 'O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4O5Y _struct_keywords.text 'damaged DNA, O6-carboxymethylguanine, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 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 4O5Y _struct_ref.pdbx_db_accession 4O5Y _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 4O5Y A 1 ? 12 ? 4O5Y 1 ? 12 ? 1 12 2 1 4O5Y B 1 ? 12 ? 4O5Y 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)' 1860 ? 1 MORE -19 ? 1 'SSA (A^2)' 4380 ? # _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_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DC 3 "O3'" ? ? ? 1_555 A C6G 4 P ? ? A DC 3 A C6G 4 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale one ? A C6G 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A C6G 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.677 ? ? covale3 covale both ? B DC 3 "O3'" ? ? ? 1_555 B C6G 4 P ? ? B DC 15 B C6G 16 1_555 ? ? ? ? ? ? ? 1.582 ? ? covale4 covale one ? B C6G 4 "O3'" ? ? ? 1_555 B DA 5 P ? ? B C6G 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.582 ? ? metalc1 metalc ? ? A DT 9 O4 ? ? ? 1_555 C K . K ? ? A DT 9 A K 101 1_555 ? ? ? ? ? ? ? 3.031 ? ? metalc2 metalc ? ? A DG 10 O6 ? ? ? 1_555 C K . K ? ? A DG 10 A K 101 1_555 ? ? ? ? ? ? ? 2.869 ? ? metalc3 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 101 A HOH 240 1_555 ? ? ? ? ? ? ? 2.767 ? ? metalc4 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 101 A HOH 249 1_555 ? ? ? ? ? ? ? 2.655 ? ? metalc5 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 101 A HOH 265 1_555 ? ? ? ? ? ? ? 3.232 ? ? metalc6 metalc ? ? C K . K ? ? ? 1_555 F HOH . O ? ? A K 101 B HOH 201 1_555 ? ? ? ? ? ? ? 3.332 ? ? metalc7 metalc ? ? C K . K ? ? ? 1_555 F HOH . O ? ? A K 101 B HOH 219 1_555 ? ? ? ? ? ? ? 2.748 ? ? metalc8 metalc ? ? C K . K ? ? ? 1_555 F HOH . O ? ? A K 101 B HOH 252 1_555 ? ? ? ? ? ? ? 3.196 ? ? metalc9 metalc ? ? E HOH . O ? ? ? 1_555 D BA . BA ? ? A HOH 217 B BA 101 1_555 ? ? ? ? ? ? ? 3.092 ? ? metalc10 metalc ? ? E HOH . O ? ? ? 1_555 D BA . BA ? ? A HOH 251 B BA 101 1_555 ? ? ? ? ? ? ? 3.399 ? ? metalc11 metalc ? ? B DT 9 O4 ? ? ? 1_555 D BA . BA ? ? B DT 21 B BA 101 1_555 ? ? ? ? ? ? ? 2.643 ? ? metalc12 metalc ? ? B DG 10 O6 ? ? ? 1_555 D BA . BA ? ? B DG 22 B BA 101 1_555 ? ? ? ? ? ? ? 3.012 ? ? metalc13 metalc ? ? D BA . BA ? ? ? 1_555 F HOH . O ? ? B BA 101 B HOH 255 1_555 ? ? ? ? ? ? ? 3.173 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 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 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O6 ? A DG 10 ? A DG 10 ? 1_555 89.8 ? 2 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 240 ? 1_555 67.8 ? 3 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 240 ? 1_555 136.4 ? 4 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 249 ? 1_555 60.2 ? 5 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 249 ? 1_555 145.3 ? 6 O ? E HOH . ? A HOH 240 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 249 ? 1_555 51.2 ? 7 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 265 ? 1_555 70.6 ? 8 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 265 ? 1_555 82.1 ? 9 O ? E HOH . ? A HOH 240 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 265 ? 1_555 55.7 ? 10 O ? E HOH . ? A HOH 249 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? E HOH . ? A HOH 265 ? 1_555 101.7 ? 11 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 201 ? 1_555 132.0 ? 12 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 201 ? 1_555 78.8 ? 13 O ? E HOH . ? A HOH 240 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 201 ? 1_555 89.0 ? 14 O ? E HOH . ? A HOH 249 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 201 ? 1_555 133.7 ? 15 O ? E HOH . ? A HOH 265 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 201 ? 1_555 61.8 ? 16 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 219 ? 1_555 163.1 ? 17 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 219 ? 1_555 98.6 ? 18 O ? E HOH . ? A HOH 240 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 219 ? 1_555 113.6 ? 19 O ? E HOH . ? A HOH 249 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 219 ? 1_555 106.6 ? 20 O ? E HOH . ? A HOH 265 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 219 ? 1_555 125.0 ? 21 O ? F HOH . ? B HOH 201 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 219 ? 1_555 64.5 ? 22 O4 ? A DT 9 ? A DT 9 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 60.0 ? 23 O6 ? A DG 10 ? A DG 10 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 99.5 ? 24 O ? E HOH . ? A HOH 240 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 100.3 ? 25 O ? E HOH . ? A HOH 249 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 51.8 ? 26 O ? E HOH . ? A HOH 265 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 130.5 ? 27 O ? F HOH . ? B HOH 201 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 167.5 ? 28 O ? F HOH . ? B HOH 219 ? 1_555 K ? C K . ? A K 101 ? 1_555 O ? F HOH . ? B HOH 252 ? 1_555 103.9 ? 29 O ? E HOH . ? A HOH 217 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O ? E HOH . ? A HOH 251 ? 1_555 61.9 ? 30 O ? E HOH . ? A HOH 217 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O4 ? B DT 9 ? B DT 21 ? 1_555 145.1 ? 31 O ? E HOH . ? A HOH 251 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O4 ? B DT 9 ? B DT 21 ? 1_555 141.2 ? 32 O ? E HOH . ? A HOH 217 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 73.4 ? 33 O ? E HOH . ? A HOH 251 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 83.5 ? 34 O4 ? B DT 9 ? B DT 21 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O6 ? B DG 10 ? B DG 22 ? 1_555 83.1 ? 35 O ? E HOH . ? A HOH 217 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O ? F HOH . ? B HOH 255 ? 1_555 92.0 ? 36 O ? E HOH . ? A HOH 251 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O ? F HOH . ? B HOH 255 ? 1_555 66.0 ? 37 O4 ? B DT 9 ? B DT 21 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O ? F HOH . ? B HOH 255 ? 1_555 120.0 ? 38 O6 ? B DG 10 ? B DG 22 ? 1_555 BA ? D BA . ? B BA 101 ? 1_555 O ? F HOH . ? B HOH 255 ? 1_555 149.5 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A K 101 ? 5 'BINDING SITE FOR RESIDUE K A 101' AC2 Software B BA 101 ? 5 'BINDING SITE FOR RESIDUE BA B 101' # 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 5 DT A 9 ? DT A 9 . ? 1_555 ? 2 AC1 5 DG A 10 ? DG A 10 . ? 1_555 ? 3 AC1 5 HOH E . ? HOH A 240 . ? 1_555 ? 4 AC1 5 HOH E . ? HOH A 249 . ? 1_555 ? 5 AC1 5 HOH F . ? HOH B 219 . ? 1_555 ? 6 AC2 5 HOH E . ? HOH A 217 . ? 1_555 ? 7 AC2 5 DT B 9 ? DT B 21 . ? 1_555 ? 8 AC2 5 DG B 10 ? DG B 22 . ? 1_555 ? 9 AC2 5 HOH F . ? HOH B 253 . ? 1_555 ? 10 AC2 5 HOH F . ? HOH B 254 . ? 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 C8 A DA 5 ? ? N9 A DA 5 ? ? 1.312 1.373 -0.061 0.008 N 2 1 C2 A DA 6 ? ? N3 A DA 6 ? ? 1.400 1.331 0.069 0.009 N 3 1 C6 A DT 7 ? ? N1 A DT 7 ? ? 1.421 1.378 0.043 0.007 N 4 1 N3 A DT 8 ? ? C4 A DT 8 ? ? 1.430 1.382 0.048 0.008 N 5 1 C5 A DC 11 ? ? C6 A DC 11 ? ? 1.291 1.339 -0.048 0.008 N 6 1 "O3'" B DG 14 ? ? "C3'" B DG 14 ? ? 1.380 1.419 -0.039 0.006 N 7 1 C6 B DT 20 ? ? N1 B DT 20 ? ? 1.432 1.378 0.054 0.007 N 8 1 "O3'" B DG 22 ? ? "C3'" B DG 22 ? ? 1.359 1.419 -0.060 0.006 N 9 1 N1 B DG 22 ? ? C2 B DG 22 ? ? 1.324 1.373 -0.049 0.008 N 10 1 C8 B DG 22 ? ? N9 B DG 22 ? ? 1.330 1.374 -0.044 0.007 N 11 1 N3 B DG 24 ? ? C4 B DG 24 ? ? 1.292 1.350 -0.058 0.007 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 N1 A DA 5 ? ? C2 A DA 5 ? ? N3 A DA 5 ? ? 126.30 129.30 -3.00 0.50 N 2 1 C2 A DA 5 ? ? N3 A DA 5 ? ? C4 A DA 5 ? ? 114.70 110.60 4.10 0.50 N 3 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 114.01 119.00 -4.99 0.60 N 4 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 126.84 122.90 3.94 0.60 N 5 1 "C3'" A DG 10 ? ? "C2'" A DG 10 ? ? "C1'" A DG 10 ? ? 95.53 102.40 -6.87 0.80 N 6 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 103.33 108.00 -4.67 0.70 N 7 1 "O4'" B DC 13 ? ? "C4'" B DC 13 ? ? "C3'" B DC 13 ? ? 102.09 104.50 -2.41 0.40 N 8 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 103.63 108.00 -4.37 0.70 N 9 1 "C3'" B DG 22 ? ? "C2'" B DG 22 ? ? "C1'" B DG 22 ? ? 97.17 102.40 -5.23 0.80 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A C6G 4 A C6G 4 ? DG ? 2 B C6G 4 B C6G 16 ? DG ? # _phasing.method MR # 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 BA BA BA N N 1 C6G P P N N 2 C6G OP1 O N N 3 C6G OP2 O N N 4 C6G "O5'" O N N 5 C6G "C5'" C N N 6 C6G "C4'" C N R 7 C6G "O4'" O N N 8 C6G "C1'" C N R 9 C6G N9 N Y N 10 C6G C8 C Y N 11 C6G N7 N Y N 12 C6G C5 C Y N 13 C6G C4 C Y N 14 C6G N3 N Y N 15 C6G C2 C Y N 16 C6G N2 N N N 17 C6G N1 N Y N 18 C6G C6 C Y N 19 C6G O6 O N N 20 C6G "C2'" C N N 21 C6G "C3'" C N S 22 C6G "O3'" O N N 23 C6G C C N N 24 C6G O O N N 25 C6G O7 O N N 26 C6G CH3 C N N 27 C6G HOP2 H N N 28 C6G "H5'" H N N 29 C6G "H5''" H N N 30 C6G "H4'" H N N 31 C6G "H1'" H N N 32 C6G H8 H N N 33 C6G H21 H N N 34 C6G H22 H N N 35 C6G "H2'" H N N 36 C6G "H2''" H N N 37 C6G "H3'" H N N 38 C6G "HO3'" H N N 39 C6G HO7 H N N 40 C6G H31 H N N 41 C6G H32 H N N 42 C6G OP3 O N N 43 C6G HOP3 H N N 44 DA OP3 O N N 45 DA P P N N 46 DA OP1 O N N 47 DA OP2 O N N 48 DA "O5'" O N N 49 DA "C5'" C N N 50 DA "C4'" C N R 51 DA "O4'" O N N 52 DA "C3'" C N S 53 DA "O3'" O N N 54 DA "C2'" C N N 55 DA "C1'" C N R 56 DA N9 N Y N 57 DA C8 C Y N 58 DA N7 N Y N 59 DA C5 C Y N 60 DA C6 C Y N 61 DA N6 N N N 62 DA N1 N Y N 63 DA C2 C Y N 64 DA N3 N Y N 65 DA C4 C Y N 66 DA HOP3 H N N 67 DA HOP2 H N N 68 DA "H5'" H N N 69 DA "H5''" H N N 70 DA "H4'" H N N 71 DA "H3'" H N N 72 DA "HO3'" H N N 73 DA "H2'" H N N 74 DA "H2''" H N N 75 DA "H1'" H N N 76 DA H8 H N N 77 DA H61 H N N 78 DA H62 H N N 79 DA H2 H N N 80 DC OP3 O N N 81 DC P P N N 82 DC OP1 O N N 83 DC OP2 O N N 84 DC "O5'" O N N 85 DC "C5'" C N N 86 DC "C4'" C N R 87 DC "O4'" O N N 88 DC "C3'" C N S 89 DC "O3'" O N N 90 DC "C2'" C N N 91 DC "C1'" C N R 92 DC N1 N N N 93 DC C2 C N N 94 DC O2 O N N 95 DC N3 N N N 96 DC C4 C N N 97 DC N4 N N N 98 DC C5 C N N 99 DC C6 C N N 100 DC HOP3 H N N 101 DC HOP2 H N N 102 DC "H5'" H N N 103 DC "H5''" H N N 104 DC "H4'" H N N 105 DC "H3'" H N N 106 DC "HO3'" H N N 107 DC "H2'" H N N 108 DC "H2''" H N N 109 DC "H1'" H N N 110 DC H41 H N N 111 DC H42 H N N 112 DC H5 H N N 113 DC H6 H N N 114 DG OP3 O N N 115 DG P P N N 116 DG OP1 O N N 117 DG OP2 O N N 118 DG "O5'" O N N 119 DG "C5'" C N N 120 DG "C4'" C N R 121 DG "O4'" O N N 122 DG "C3'" C N S 123 DG "O3'" O N N 124 DG "C2'" C N N 125 DG "C1'" C N R 126 DG N9 N Y N 127 DG C8 C Y N 128 DG N7 N Y N 129 DG C5 C Y N 130 DG C6 C N N 131 DG O6 O N N 132 DG N1 N N N 133 DG C2 C N N 134 DG N2 N N N 135 DG N3 N N N 136 DG C4 C Y N 137 DG HOP3 H N N 138 DG HOP2 H N N 139 DG "H5'" H N N 140 DG "H5''" H N N 141 DG "H4'" H N N 142 DG "H3'" H N N 143 DG "HO3'" H N N 144 DG "H2'" H N N 145 DG "H2''" H N N 146 DG "H1'" H N N 147 DG H8 H N N 148 DG H1 H N N 149 DG H21 H N N 150 DG H22 H N N 151 DT OP3 O N N 152 DT P P N N 153 DT OP1 O N N 154 DT OP2 O N N 155 DT "O5'" O N N 156 DT "C5'" C N N 157 DT "C4'" C N R 158 DT "O4'" O N N 159 DT "C3'" C N S 160 DT "O3'" O N N 161 DT "C2'" C N N 162 DT "C1'" C N R 163 DT N1 N N N 164 DT C2 C N N 165 DT O2 O N N 166 DT N3 N N N 167 DT C4 C N N 168 DT O4 O N N 169 DT C5 C N N 170 DT C7 C N N 171 DT C6 C N N 172 DT HOP3 H N N 173 DT HOP2 H N N 174 DT "H5'" H N N 175 DT "H5''" H N N 176 DT "H4'" H N N 177 DT "H3'" H N N 178 DT "HO3'" H N N 179 DT "H2'" H N N 180 DT "H2''" H N N 181 DT "H1'" H N N 182 DT H3 H N N 183 DT H71 H N N 184 DT H72 H N N 185 DT H73 H N N 186 DT H6 H N N 187 HOH O O N N 188 HOH H1 H N N 189 HOH H2 H N N 190 K K K N N 191 # 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 C6G OP1 P doub N N 1 C6G P OP2 sing N N 2 C6G P "O5'" sing N N 3 C6G O C doub N N 4 C6G C O7 sing N N 5 C6G C CH3 sing N N 6 C6G "O5'" "C5'" sing N N 7 C6G "C5'" "C4'" sing N N 8 C6G N7 C8 doub Y N 9 C6G N7 C5 sing Y N 10 C6G C8 N9 sing Y N 11 C6G O6 CH3 sing N N 12 C6G O6 C6 sing N N 13 C6G "C2'" "C3'" sing N N 14 C6G "C2'" "C1'" sing N N 15 C6G C5 C6 doub Y N 16 C6G C5 C4 sing Y N 17 C6G C6 N1 sing Y N 18 C6G N9 C4 sing Y N 19 C6G N9 "C1'" sing N N 20 C6G "C3'" "C4'" sing N N 21 C6G "C3'" "O3'" sing N N 22 C6G C4 N3 doub Y N 23 C6G "C4'" "O4'" sing N N 24 C6G N1 C2 doub Y N 25 C6G "C1'" "O4'" sing N N 26 C6G N3 C2 sing Y N 27 C6G C2 N2 sing N N 28 C6G OP2 HOP2 sing N N 29 C6G "C5'" "H5'" sing N N 30 C6G "C5'" "H5''" sing N N 31 C6G "C4'" "H4'" sing N N 32 C6G "C1'" "H1'" sing N N 33 C6G C8 H8 sing N N 34 C6G N2 H21 sing N N 35 C6G N2 H22 sing N N 36 C6G "C2'" "H2'" sing N N 37 C6G "C2'" "H2''" sing N N 38 C6G "C3'" "H3'" sing N N 39 C6G "O3'" "HO3'" sing N N 40 C6G O7 HO7 sing N N 41 C6G CH3 H31 sing N N 42 C6G CH3 H32 sing N N 43 C6G P OP3 sing N N 44 C6G OP3 HOP3 sing N N 45 DA OP3 P sing N N 46 DA OP3 HOP3 sing N N 47 DA P OP1 doub N N 48 DA P OP2 sing N N 49 DA P "O5'" sing N N 50 DA OP2 HOP2 sing N N 51 DA "O5'" "C5'" sing N N 52 DA "C5'" "C4'" sing N N 53 DA "C5'" "H5'" sing N N 54 DA "C5'" "H5''" sing N N 55 DA "C4'" "O4'" sing N N 56 DA "C4'" "C3'" sing N N 57 DA "C4'" "H4'" sing N N 58 DA "O4'" "C1'" sing N N 59 DA "C3'" "O3'" sing N N 60 DA "C3'" "C2'" sing N N 61 DA "C3'" "H3'" sing N N 62 DA "O3'" "HO3'" sing N N 63 DA "C2'" "C1'" sing N N 64 DA "C2'" "H2'" sing N N 65 DA "C2'" "H2''" sing N N 66 DA "C1'" N9 sing N N 67 DA "C1'" "H1'" sing N N 68 DA N9 C8 sing Y N 69 DA N9 C4 sing Y N 70 DA C8 N7 doub Y N 71 DA C8 H8 sing N N 72 DA N7 C5 sing Y N 73 DA C5 C6 sing Y N 74 DA C5 C4 doub Y N 75 DA C6 N6 sing N N 76 DA C6 N1 doub Y N 77 DA N6 H61 sing N N 78 DA N6 H62 sing N N 79 DA N1 C2 sing Y N 80 DA C2 N3 doub Y N 81 DA C2 H2 sing N N 82 DA N3 C4 sing Y N 83 DC OP3 P sing N N 84 DC OP3 HOP3 sing N N 85 DC P OP1 doub N N 86 DC P OP2 sing N N 87 DC P "O5'" sing N N 88 DC OP2 HOP2 sing N N 89 DC "O5'" "C5'" sing N N 90 DC "C5'" "C4'" sing N N 91 DC "C5'" "H5'" sing N N 92 DC "C5'" "H5''" sing N N 93 DC "C4'" "O4'" sing N N 94 DC "C4'" "C3'" sing N N 95 DC "C4'" "H4'" sing N N 96 DC "O4'" "C1'" sing N N 97 DC "C3'" "O3'" sing N N 98 DC "C3'" "C2'" sing N N 99 DC "C3'" "H3'" sing N N 100 DC "O3'" "HO3'" sing N N 101 DC "C2'" "C1'" sing N N 102 DC "C2'" "H2'" sing N N 103 DC "C2'" "H2''" sing N N 104 DC "C1'" N1 sing N N 105 DC "C1'" "H1'" sing N N 106 DC N1 C2 sing N N 107 DC N1 C6 sing N N 108 DC C2 O2 doub N N 109 DC C2 N3 sing N N 110 DC N3 C4 doub N N 111 DC C4 N4 sing N N 112 DC C4 C5 sing N N 113 DC N4 H41 sing N N 114 DC N4 H42 sing N N 115 DC C5 C6 doub N N 116 DC C5 H5 sing N N 117 DC C6 H6 sing N N 118 DG OP3 P sing N N 119 DG OP3 HOP3 sing N N 120 DG P OP1 doub N N 121 DG P OP2 sing N N 122 DG P "O5'" sing N N 123 DG OP2 HOP2 sing N N 124 DG "O5'" "C5'" sing N N 125 DG "C5'" "C4'" sing N N 126 DG "C5'" "H5'" sing N N 127 DG "C5'" "H5''" sing N N 128 DG "C4'" "O4'" sing N N 129 DG "C4'" "C3'" sing N N 130 DG "C4'" "H4'" sing N N 131 DG "O4'" "C1'" sing N N 132 DG "C3'" "O3'" sing N N 133 DG "C3'" "C2'" sing N N 134 DG "C3'" "H3'" sing N N 135 DG "O3'" "HO3'" sing N N 136 DG "C2'" "C1'" sing N N 137 DG "C2'" "H2'" sing N N 138 DG "C2'" "H2''" sing N N 139 DG "C1'" N9 sing N N 140 DG "C1'" "H1'" sing N N 141 DG N9 C8 sing Y N 142 DG N9 C4 sing Y N 143 DG C8 N7 doub Y N 144 DG C8 H8 sing N N 145 DG N7 C5 sing Y N 146 DG C5 C6 sing N N 147 DG C5 C4 doub Y N 148 DG C6 O6 doub N N 149 DG C6 N1 sing N N 150 DG N1 C2 sing N N 151 DG N1 H1 sing N N 152 DG C2 N2 sing N N 153 DG C2 N3 doub N N 154 DG N2 H21 sing N N 155 DG N2 H22 sing N N 156 DG N3 C4 sing N N 157 DT OP3 P sing N N 158 DT OP3 HOP3 sing N N 159 DT P OP1 doub N N 160 DT P OP2 sing N N 161 DT P "O5'" sing N N 162 DT OP2 HOP2 sing N N 163 DT "O5'" "C5'" sing N N 164 DT "C5'" "C4'" sing N N 165 DT "C5'" "H5'" sing N N 166 DT "C5'" "H5''" sing N N 167 DT "C4'" "O4'" sing N N 168 DT "C4'" "C3'" sing N N 169 DT "C4'" "H4'" sing N N 170 DT "O4'" "C1'" sing N N 171 DT "C3'" "O3'" sing N N 172 DT "C3'" "C2'" sing N N 173 DT "C3'" "H3'" sing N N 174 DT "O3'" "HO3'" sing N N 175 DT "C2'" "C1'" sing N N 176 DT "C2'" "H2'" sing N N 177 DT "C2'" "H2''" sing N N 178 DT "C1'" N1 sing N N 179 DT "C1'" "H1'" sing N N 180 DT N1 C2 sing N N 181 DT N1 C6 sing N N 182 DT C2 O2 doub N N 183 DT C2 N3 sing N N 184 DT N3 C4 sing N N 185 DT N3 H3 sing N N 186 DT C4 O4 doub N N 187 DT C4 C5 sing N N 188 DT C5 C7 sing N N 189 DT C5 C6 doub N N 190 DT C7 H71 sing N N 191 DT C7 H72 sing N N 192 DT C7 H73 sing N N 193 DT C6 H6 sing N N 194 HOH O H1 sing N N 195 HOH O H2 sing N N 196 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4O5Y 'double helix' 4O5Y 'b-form double helix' 4O5Y 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.191 -0.255 0.349 -3.140 -6.150 -2.172 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.128 -0.225 0.197 -4.950 -8.198 -6.498 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.182 -0.146 0.110 0.856 0.040 2.266 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.006 -0.045 -0.037 6.282 -25.379 3.519 4 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.021 -0.175 0.072 0.889 -19.462 3.894 5 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.012 -0.155 0.054 -1.700 -19.952 2.539 6 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.094 -0.084 0.065 -6.815 -18.549 3.666 7 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DG 10 1_555 B DC 3 1_555 -0.105 -0.159 0.145 5.617 2.540 -0.398 8 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.136 -0.187 0.236 3.846 -15.243 -0.450 9 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.180 -0.201 0.349 6.968 -10.228 -0.318 10 A_DG12:DC13_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 DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.365 0.335 3.391 0.458 -4.782 40.224 1.036 0.579 3.327 -6.924 -0.663 40.498 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 1.188 0.382 3.287 1.911 -3.629 38.352 1.031 -1.560 3.292 -5.504 -2.899 38.563 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DA 5 1_555 B DT 8 1_555 -0.183 0.360 6.537 4.161 6.902 59.885 -0.317 0.589 6.515 6.880 -4.148 60.375 3 AA_DC3DA5:DT20DG22_BB A 3 ? B 22 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.139 0.001 3.233 -1.294 0.389 40.383 -0.042 -0.344 3.227 0.563 1.874 40.405 4 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.037 -0.573 3.284 0.101 0.763 31.237 -1.209 0.088 3.269 1.416 -0.188 31.246 5 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.099 -0.275 3.326 0.640 -1.887 38.132 -0.178 0.234 3.333 -2.886 -0.978 38.182 6 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DG 10 1_555 B DC 3 1_555 0.037 0.193 6.334 -2.491 -0.267 65.995 0.198 -0.229 6.328 -0.245 2.286 66.038 7 AA_DT8DG10:DC15DA17_BB A 8 ? B 17 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.107 0.790 3.402 -1.705 -9.199 43.658 1.906 1.299 3.219 -12.203 2.261 44.601 8 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 0.384 0.450 3.203 0.038 1.239 35.379 0.561 -0.627 3.217 2.038 -0.062 35.400 9 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 4O5Y _atom_sites.fract_transf_matrix[1][1] 0.038525 _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] 0.024082 _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] 0.015458 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol BA C K N O P # loop_