data_361D # _entry.id 361D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 361D pdb_0000361d 10.2210/pdb361d/pdb RCSB URT068 ? ? WWPDB D_1000178831 ? ? # 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 1998-07-01 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-21 5 'Structure model' 1 4 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 5 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' diffrn_source 5 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 361D _pdbx_database_status.recvd_initial_deposition_date 1997-11-10 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Perbandt, M.' 1 'Nolte, A.' 2 'Lorenz, S.' 3 'Erdmann, V.A.' 4 'Betzel, C.' 5 # _citation.id primary _citation.title 'Crystal structure of domain E of Thermus flavus 5S rRNA: a helical RNA structure including a hairpin loop.' _citation.journal_abbrev 'FEBS Lett.' _citation.journal_volume 429 _citation.page_first 211 _citation.page_last 215 _citation.year 1998 _citation.journal_id_ASTM FEBLAL _citation.country NE _citation.journal_id_ISSN 0014-5793 _citation.journal_id_CSD 0165 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9650592 _citation.pdbx_database_id_DOI '10.1016/S0014-5793(98)00436-0' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Perbandt, M.' 1 ? primary 'Nolte, A.' 2 ? primary 'Lorenz, S.' 3 ? primary 'Bald, R.' 4 ? primary 'Betzel, C.' 5 ? primary 'Erdmann, V.A.' 6 ? # 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(*CP*UP*GP*GP*GP*CP*GP*GP*GP*CP*GP*AP*CP*CP*GP*CP*C P*UP*GP*G)-3') ; 6484.910 2 ? ? ? ? 2 water nat water 18.015 221 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'DOMAIN E OF THERMUS FLAVUS 5S RRNA' # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CUGGGCGGGCGACCGCCUGG _entity_poly.pdbx_seq_one_letter_code_can CUGGGCGGGCGACCGCCUGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 G n 1 4 G n 1 5 G n 1 6 C n 1 7 G n 1 8 G n 1 9 G n 1 10 C n 1 11 G n 1 12 A n 1 13 C n 1 14 C n 1 15 G n 1 16 C n 1 17 C n 1 18 U n 1 19 G n 1 20 G n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 79 79 C C A . n A 1 2 U 2 80 80 U U A . n A 1 3 G 3 81 81 G G A . n A 1 4 G 4 82 82 G G A . n A 1 5 G 5 83 83 G G A . n A 1 6 C 6 84 84 C C A . n A 1 7 G 7 85 85 G G A . n A 1 8 G 8 86 86 G G A . n A 1 9 G 9 87 87 G G A . n A 1 10 C 10 88 88 C C A . n A 1 11 G 11 89 89 G G A . n A 1 12 A 12 89 89 A A A A n A 1 13 C 13 90 90 C C A . n A 1 14 C 14 91 91 C C A . n A 1 15 G 15 92 92 G G A . n A 1 16 C 16 93 93 C C A . n A 1 17 C 17 94 94 C C A . n A 1 18 U 18 95 95 U U A . n A 1 19 G 19 96 96 G G A . n A 1 20 G 20 97 97 G G A . n B 1 1 C 1 79 79 C C B . n B 1 2 U 2 80 80 U U B . n B 1 3 G 3 81 81 G G B . n B 1 4 G 4 82 82 G G B . n B 1 5 G 5 83 83 G G B . n B 1 6 C 6 84 84 C C B . n B 1 7 G 7 85 85 G G B . n B 1 8 G 8 86 86 G G B . n B 1 9 G 9 87 87 G G B . n B 1 10 C 10 88 88 C C B . n B 1 11 G 11 89 89 G G B . n B 1 12 A 12 89 89 A A B A n B 1 13 C 13 90 90 C C B . n B 1 14 C 14 91 91 C C B . n B 1 15 G 15 92 92 G G B . n B 1 16 C 16 93 93 C C B . n B 1 17 C 17 94 94 C C B . n B 1 18 U 18 95 95 U U B . n B 1 19 G 19 96 96 G G B . n B 1 20 G 20 97 97 G G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 101 101 HOH HOH A . C 2 HOH 2 102 102 HOH HOH A . C 2 HOH 3 103 103 HOH HOH A . C 2 HOH 4 104 104 HOH HOH A . C 2 HOH 5 105 105 HOH HOH A . C 2 HOH 6 106 106 HOH HOH A . C 2 HOH 7 107 107 HOH HOH A . C 2 HOH 8 110 110 HOH HOH A . C 2 HOH 9 111 111 HOH HOH A . C 2 HOH 10 112 112 HOH HOH A . C 2 HOH 11 113 113 HOH HOH A . C 2 HOH 12 114 114 HOH HOH A . C 2 HOH 13 115 115 HOH HOH A . C 2 HOH 14 116 116 HOH HOH A . C 2 HOH 15 117 117 HOH HOH A . C 2 HOH 16 118 118 HOH HOH A . C 2 HOH 17 119 119 HOH HOH A . C 2 HOH 18 120 120 HOH HOH A . C 2 HOH 19 121 121 HOH HOH A . C 2 HOH 20 122 122 HOH HOH A . C 2 HOH 21 123 123 HOH HOH A . C 2 HOH 22 124 124 HOH HOH A . C 2 HOH 23 125 125 HOH HOH A . C 2 HOH 24 126 126 HOH HOH A . C 2 HOH 25 127 127 HOH HOH A . C 2 HOH 26 128 128 HOH HOH A . C 2 HOH 27 129 129 HOH HOH A . C 2 HOH 28 130 130 HOH HOH A . C 2 HOH 29 131 131 HOH HOH A . C 2 HOH 30 132 132 HOH HOH A . C 2 HOH 31 134 134 HOH HOH A . C 2 HOH 32 136 136 HOH HOH A . C 2 HOH 33 137 137 HOH HOH A . C 2 HOH 34 138 138 HOH HOH A . C 2 HOH 35 139 139 HOH HOH A . C 2 HOH 36 140 140 HOH HOH A . C 2 HOH 37 141 141 HOH HOH A . C 2 HOH 38 142 142 HOH HOH A . C 2 HOH 39 143 143 HOH HOH A . C 2 HOH 40 144 144 HOH HOH A . C 2 HOH 41 145 145 HOH HOH A . C 2 HOH 42 146 146 HOH HOH A . C 2 HOH 43 147 147 HOH HOH A . C 2 HOH 44 148 148 HOH HOH A . C 2 HOH 45 149 149 HOH HOH A . C 2 HOH 46 150 150 HOH HOH A . C 2 HOH 47 151 151 HOH HOH A . C 2 HOH 48 152 152 HOH HOH A . C 2 HOH 49 155 155 HOH HOH A . C 2 HOH 50 156 156 HOH HOH A . C 2 HOH 51 157 157 HOH HOH A . C 2 HOH 52 158 158 HOH HOH A . C 2 HOH 53 159 159 HOH HOH A . C 2 HOH 54 160 160 HOH HOH A . C 2 HOH 55 161 161 HOH HOH A . C 2 HOH 56 163 163 HOH HOH A . C 2 HOH 57 164 164 HOH HOH A . C 2 HOH 58 165 165 HOH HOH A . C 2 HOH 59 166 166 HOH HOH A . C 2 HOH 60 167 167 HOH HOH A . C 2 HOH 61 168 168 HOH HOH A . C 2 HOH 62 169 169 HOH HOH A . C 2 HOH 63 170 170 HOH HOH A . C 2 HOH 64 171 171 HOH HOH A . C 2 HOH 65 172 172 HOH HOH A . C 2 HOH 66 173 173 HOH HOH A . C 2 HOH 67 174 174 HOH HOH A . C 2 HOH 68 175 175 HOH HOH A . C 2 HOH 69 176 176 HOH HOH A . C 2 HOH 70 177 177 HOH HOH A . C 2 HOH 71 178 178 HOH HOH A . C 2 HOH 72 179 179 HOH HOH A . C 2 HOH 73 180 180 HOH HOH A . C 2 HOH 74 181 181 HOH HOH A . C 2 HOH 75 182 182 HOH HOH A . C 2 HOH 76 183 183 HOH HOH A . C 2 HOH 77 184 184 HOH HOH A . C 2 HOH 78 185 185 HOH HOH A . C 2 HOH 79 186 186 HOH HOH A . C 2 HOH 80 187 187 HOH HOH A . C 2 HOH 81 188 188 HOH HOH A . C 2 HOH 82 189 189 HOH HOH A . C 2 HOH 83 190 190 HOH HOH A . C 2 HOH 84 191 191 HOH HOH A . C 2 HOH 85 192 192 HOH HOH A . C 2 HOH 86 193 193 HOH HOH A . C 2 HOH 87 194 194 HOH HOH A . C 2 HOH 88 195 195 HOH HOH A . C 2 HOH 89 196 196 HOH HOH A . C 2 HOH 90 197 197 HOH HOH A . C 2 HOH 91 198 198 HOH HOH A . C 2 HOH 92 199 199 HOH HOH A . C 2 HOH 93 200 200 HOH HOH A . C 2 HOH 94 201 201 HOH HOH A . C 2 HOH 95 202 202 HOH HOH A . C 2 HOH 96 203 203 HOH HOH A . C 2 HOH 97 204 204 HOH HOH A . C 2 HOH 98 205 205 HOH HOH A . C 2 HOH 99 206 206 HOH HOH A . C 2 HOH 100 207 207 HOH HOH A . C 2 HOH 101 208 208 HOH HOH A . C 2 HOH 102 209 209 HOH HOH A . C 2 HOH 103 210 210 HOH HOH A . C 2 HOH 104 211 211 HOH HOH A . C 2 HOH 105 212 212 HOH HOH A . C 2 HOH 106 213 213 HOH HOH A . C 2 HOH 107 214 214 HOH HOH A . C 2 HOH 108 215 215 HOH HOH A . C 2 HOH 109 237 237 HOH HOH A . C 2 HOH 110 243 243 HOH HOH A . C 2 HOH 111 246 246 HOH HOH A . C 2 HOH 112 247 247 HOH HOH A . C 2 HOH 113 250 250 HOH HOH A . C 2 HOH 114 252 252 HOH HOH A . C 2 HOH 115 258 258 HOH HOH A . C 2 HOH 116 263 263 HOH HOH A . C 2 HOH 117 279 279 HOH HOH A . C 2 HOH 118 283 283 HOH HOH A . C 2 HOH 119 291 291 HOH HOH A . C 2 HOH 120 315 315 HOH HOH A . D 2 HOH 1 108 108 HOH HOH B . D 2 HOH 2 109 109 HOH HOH B . D 2 HOH 3 133 133 HOH HOH B . D 2 HOH 4 135 135 HOH HOH B . D 2 HOH 5 153 153 HOH HOH B . D 2 HOH 6 154 154 HOH HOH B . D 2 HOH 7 162 162 HOH HOH B . D 2 HOH 8 216 216 HOH HOH B . D 2 HOH 9 217 217 HOH HOH B . D 2 HOH 10 218 218 HOH HOH B . D 2 HOH 11 219 219 HOH HOH B . D 2 HOH 12 220 220 HOH HOH B . D 2 HOH 13 221 221 HOH HOH B . D 2 HOH 14 222 222 HOH HOH B . D 2 HOH 15 223 223 HOH HOH B . D 2 HOH 16 224 224 HOH HOH B . D 2 HOH 17 225 225 HOH HOH B . D 2 HOH 18 226 226 HOH HOH B . D 2 HOH 19 227 227 HOH HOH B . D 2 HOH 20 228 228 HOH HOH B . D 2 HOH 21 229 229 HOH HOH B . D 2 HOH 22 230 230 HOH HOH B . D 2 HOH 23 231 231 HOH HOH B . D 2 HOH 24 232 232 HOH HOH B . D 2 HOH 25 233 233 HOH HOH B . D 2 HOH 26 234 234 HOH HOH B . D 2 HOH 27 235 235 HOH HOH B . D 2 HOH 28 236 236 HOH HOH B . D 2 HOH 29 238 238 HOH HOH B . D 2 HOH 30 239 239 HOH HOH B . D 2 HOH 31 240 240 HOH HOH B . D 2 HOH 32 241 241 HOH HOH B . D 2 HOH 33 242 242 HOH HOH B . D 2 HOH 34 244 244 HOH HOH B . D 2 HOH 35 245 245 HOH HOH B . D 2 HOH 36 248 248 HOH HOH B . D 2 HOH 37 249 249 HOH HOH B . D 2 HOH 38 251 251 HOH HOH B . D 2 HOH 39 253 253 HOH HOH B . D 2 HOH 40 254 254 HOH HOH B . D 2 HOH 41 255 255 HOH HOH B . D 2 HOH 42 256 256 HOH HOH B . D 2 HOH 43 257 257 HOH HOH B . D 2 HOH 44 259 259 HOH HOH B . D 2 HOH 45 260 260 HOH HOH B . D 2 HOH 46 261 261 HOH HOH B . D 2 HOH 47 262 262 HOH HOH B . D 2 HOH 48 264 264 HOH HOH B . D 2 HOH 49 265 265 HOH HOH B . D 2 HOH 50 266 266 HOH HOH B . D 2 HOH 51 267 267 HOH HOH B . D 2 HOH 52 268 268 HOH HOH B . D 2 HOH 53 269 269 HOH HOH B . D 2 HOH 54 270 270 HOH HOH B . D 2 HOH 55 271 271 HOH HOH B . D 2 HOH 56 272 272 HOH HOH B . D 2 HOH 57 273 273 HOH HOH B . D 2 HOH 58 274 274 HOH HOH B . D 2 HOH 59 275 275 HOH HOH B . D 2 HOH 60 276 276 HOH HOH B . D 2 HOH 61 277 277 HOH HOH B . D 2 HOH 62 278 278 HOH HOH B . D 2 HOH 63 280 280 HOH HOH B . D 2 HOH 64 281 281 HOH HOH B . D 2 HOH 65 282 282 HOH HOH B . D 2 HOH 66 284 284 HOH HOH B . D 2 HOH 67 285 285 HOH HOH B . D 2 HOH 68 286 286 HOH HOH B . D 2 HOH 69 287 287 HOH HOH B . D 2 HOH 70 288 288 HOH HOH B . D 2 HOH 71 289 289 HOH HOH B . D 2 HOH 72 290 290 HOH HOH B . D 2 HOH 73 292 292 HOH HOH B . D 2 HOH 74 293 293 HOH HOH B . D 2 HOH 75 294 294 HOH HOH B . D 2 HOH 76 295 295 HOH HOH B . D 2 HOH 77 296 296 HOH HOH B . D 2 HOH 78 297 297 HOH HOH B . D 2 HOH 79 298 298 HOH HOH B . D 2 HOH 80 299 299 HOH HOH B . D 2 HOH 81 300 300 HOH HOH B . D 2 HOH 82 301 301 HOH HOH B . D 2 HOH 83 302 302 HOH HOH B . D 2 HOH 84 303 303 HOH HOH B . D 2 HOH 85 304 304 HOH HOH B . D 2 HOH 86 305 305 HOH HOH B . D 2 HOH 87 306 306 HOH HOH B . D 2 HOH 88 307 307 HOH HOH B . D 2 HOH 89 308 308 HOH HOH B . D 2 HOH 90 309 309 HOH HOH B . D 2 HOH 91 310 310 HOH HOH B . D 2 HOH 92 311 311 HOH HOH B . D 2 HOH 93 312 312 HOH HOH B . D 2 HOH 94 313 313 HOH HOH B . D 2 HOH 95 314 314 HOH HOH B . D 2 HOH 96 316 316 HOH HOH B . D 2 HOH 97 317 317 HOH HOH B . D 2 HOH 98 318 318 HOH HOH B . D 2 HOH 99 319 319 HOH HOH B . D 2 HOH 100 320 320 HOH HOH B . D 2 HOH 101 321 321 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 Y 0 A G 97 ? P ? A G 20 P 2 1 Y 0 A G 97 ? OP1 ? A G 20 OP1 3 1 Y 0 A G 97 ? OP2 ? A G 20 OP2 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 X-PLOR refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 361D _cell.length_a 42.680 _cell.length_b 42.680 _cell.length_c 161.200 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 361D _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 # _exptl.entry_id 361D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.20 _exptl_crystal.density_percent_sol 54.0000 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 277.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1995-01-01 _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 . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X11' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X11 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 361D _reflns.observed_criterion_sigma_I 3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30.000 _reflns.d_resolution_high 2.800 _reflns.number_obs 4702 _reflns.number_all ? _reflns.percent_possible_obs 93.600 _reflns.pdbx_Rmerge_I_obs 0.0720000 _reflns.pdbx_Rsym_value 0.0720000 _reflns.pdbx_netI_over_sigmaI 8.7500 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.250 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.800 _reflns_shell.d_res_low 2.900 _reflns_shell.percent_possible_all 96.00 _reflns_shell.Rmerge_I_obs 0.4480000 _reflns_shell.pdbx_Rsym_value 0.4480000 _reflns_shell.meanI_over_sigI_obs 1.860 _reflns_shell.pdbx_redundancy 1.870 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 361D _refine.ls_number_reflns_obs 3667 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 15.000 _refine.ls_d_res_high 3.000 _refine.ls_percent_reflns_obs 97.100 _refine.ls_R_factor_obs 0.2410000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2410000 _refine.ls_R_factor_R_free 0.3180000 _refine.ls_R_factor_R_free_error 0.023 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 183 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 30.40 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model '16NT FRAGMENT OF DOMAINA FROM 5SRNA' _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 361D _refine_analyze.Luzzati_coordinate_error_obs 0.45 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 858 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 221 _refine_hist.number_atoms_total 1079 _refine_hist.d_res_high 3.000 _refine_hist.d_res_low 15.000 # 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 x_bond_d 0.010 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.73 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 25.1 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 3.17 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 8 _refine_ls_shell.d_res_high 3.00 _refine_ls_shell.d_res_low 3.30 _refine_ls_shell.number_reflns_R_work 358 _refine_ls_shell.R_factor_R_work 0.3210000 _refine_ls_shell.percent_reflns_obs 96.20 _refine_ls_shell.R_factor_R_free 0.3650000 _refine_ls_shell.R_factor_R_free_error 0.06 _refine_ls_shell.percent_reflns_R_free 5.00 _refine_ls_shell.number_reflns_R_free 18 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _pdbx_xplor_file.serial_no 1 _pdbx_xplor_file.param_file DNA-RNA.PARAM _pdbx_xplor_file.topol_file DNA-RNA.TOP _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 361D _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 361D _struct.title 'CRYSTAL STRUCTURE OF DOMAIN E OF THERMUS FLAVUS 5S RRNA: A HELICAL RNA-STRUCTURE INCLUDING A TETRALOOP' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 361D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, SINGLE STRAND, TETRALOOP, HAIRPIN, MISMATCHED' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 361D _struct_ref.pdbx_db_accession 361D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 361D A 1 ? 20 ? 361D 79 ? 97 ? 79 97 2 1 361D B 1 ? 20 ? 361D 79 ? 97 ? 79 97 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 author_defined_assembly ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C 2 1 B,D # _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_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? # 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 hydrog1 hydrog ? ? A U 2 O4 ? ? ? 1_555 A G 19 N1 ? ? A U 80 A G 96 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog2 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 17 O2 ? ? A G 82 A C 94 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog3 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 83 A C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 83 A C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 83 A C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 17 O2 ? ? A G 83 A C 94 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog7 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 84 A G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 84 A G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 84 A G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 7 N1 ? ? ? 1_555 A C 14 N3 ? ? A G 85 A C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 7 N2 ? ? ? 1_555 A C 14 O2 ? ? A G 85 A C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 7 O6 ? ? ? 1_555 A C 14 N4 ? ? A G 85 A C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 86 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 86 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 86 A C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 9 N3 ? ? ? 1_555 A A 12 N6 ? A A G 87 A A 89 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog17 hydrog ? ? A G 9 N1 ? ? ? 1_555 B G 20 O6 ? ? A G 87 B G 97 1_555 ? ? ? ? ? ? TYPE_3_PAIR ? ? ? hydrog18 hydrog ? ? A G 9 O6 ? ? ? 1_555 B G 20 N1 ? ? A G 87 B G 97 1_555 ? ? ? ? ? ? TYPE_3_PAIR ? ? ? hydrog19 hydrog ? ? B C 1 N4 ? ? ? 1_555 B G 20 N7 ? ? B C 79 B G 97 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog20 hydrog ? ? B U 2 N3 ? ? ? 1_555 B G 19 O6 ? ? B U 80 B G 96 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? B U 2 O2 ? ? ? 1_555 B G 19 N1 ? ? B U 80 B G 96 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? B G 4 N1 ? ? ? 1_555 B C 17 O2 ? ? B G 82 B C 94 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog23 hydrog ? ? B G 5 N1 ? ? ? 1_555 B C 16 N3 ? ? B G 83 B C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B G 5 N2 ? ? ? 1_555 B C 16 O2 ? ? B G 83 B C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B G 5 O6 ? ? ? 1_555 B C 16 N4 ? ? B G 83 B C 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B C 6 N3 ? ? ? 1_555 B G 15 N1 ? ? B C 84 B G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B C 6 N4 ? ? ? 1_555 B G 15 O6 ? ? B C 84 B G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B C 6 O2 ? ? ? 1_555 B G 15 N2 ? ? B C 84 B G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B G 7 N1 ? ? ? 1_555 B C 14 N3 ? ? B G 85 B C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B G 7 N2 ? ? ? 1_555 B C 14 O2 ? ? B G 85 B C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B G 7 O6 ? ? ? 1_555 B C 14 N4 ? ? B G 85 B C 91 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B G 8 N1 ? ? ? 1_555 B C 13 N3 ? ? B G 86 B C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 8 N2 ? ? ? 1_555 B C 13 O2 ? ? B G 86 B C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B G 8 O6 ? ? ? 1_555 B C 13 N4 ? ? B G 86 B C 90 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B G 9 N3 ? ? ? 1_555 B A 12 N6 ? A B G 87 B A 89 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N3 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 G _pdbx_validate_close_contact.auth_seq_id_1 89 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 310 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.18 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A U 80 ? ? "C1'" A U 80 ? ? N1 A U 80 ? ? 113.61 108.50 5.11 0.70 N 2 1 N9 A G 86 ? ? "C1'" A G 86 ? ? "C2'" A G 86 ? ? 124.89 114.00 10.89 1.30 N 3 1 "C5'" B G 97 ? ? "C4'" B G 97 ? ? "O4'" B G 97 ? ? 115.26 109.80 5.46 0.90 N 4 1 "C4'" B G 97 ? ? "C3'" B G 97 ? ? "O3'" B G 97 ? ? 129.65 113.00 16.65 2.00 N 5 1 N9 B G 97 ? ? "C1'" B G 97 ? ? "C2'" B G 97 ? ? 105.01 112.00 -6.99 1.10 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 86 ? ? 0.066 'SIDE CHAIN' 2 1 G A 89 ? ? 0.067 'SIDE CHAIN' 3 1 G A 92 ? ? 0.062 'SIDE CHAIN' 4 1 U A 95 ? ? 0.063 'SIDE CHAIN' 5 1 G B 89 ? ? 0.079 'SIDE CHAIN' 6 1 G B 96 ? ? 0.052 'SIDE CHAIN' 7 1 G B 97 ? ? 0.081 'SIDE CHAIN' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 361D 'double helix' 361D 'a-form double helix' 361D tetraloop 361D '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 U 2 1_555 A G 19 1_555 -2.980 -3.575 -0.583 9.457 2.251 84.189 1 A_U80:G96_A A 80 ? A 96 ? ? 1 1 A G 4 1_555 A C 17 1_555 -1.525 -0.742 0.416 9.950 0.596 -27.600 2 A_G82:C94_A A 82 ? A 94 ? ? 1 1 A G 5 1_555 A C 16 1_555 1.211 -0.581 -0.739 0.784 -0.714 -10.526 3 A_G83:C93_A A 83 ? A 93 ? 19 1 1 A C 6 1_555 A G 15 1_555 -1.534 -0.568 0.122 7.449 -3.503 -16.099 4 A_C84:G92_A A 84 ? A 92 ? 19 1 1 A G 7 1_555 A C 14 1_555 -1.067 -0.716 -0.257 -6.861 2.935 -8.364 5 A_G85:C91_A A 85 ? A 91 ? 19 1 1 A G 8 1_555 A C 13 1_555 0.469 0.192 0.219 4.596 -1.769 9.076 6 A_G86:C90_A A 86 ? A 90 ? 19 1 1 A G 9 1_555 B G 20 1_555 -0.454 -2.774 -0.240 34.838 16.333 153.108 7 A_G87:G97_B A 87 ? B 97 ? 3 ? 1 B U 2 1_555 B G 19 1_555 1.467 -0.407 -0.018 -4.413 -1.678 -10.661 8 B_U80:G96_B B 80 ? B 96 ? 28 ? 1 B G 4 1_555 B C 17 1_555 -1.693 -0.634 0.562 11.496 -0.984 -27.323 9 B_G82:C94_B B 82 ? B 94 ? ? 1 1 B G 5 1_555 B C 16 1_555 1.115 -0.573 -0.480 -0.194 1.101 -8.723 10 B_G83:C93_B B 83 ? B 93 ? 19 1 1 B C 6 1_555 B G 15 1_555 -1.452 -0.542 0.084 10.883 -4.031 -17.108 11 B_C84:G92_B B 84 ? B 92 ? 19 1 1 B G 7 1_555 B C 14 1_555 -1.025 -0.561 0.049 0.047 -0.204 -8.688 12 B_G85:C91_B B 85 ? B 91 ? 19 1 1 B G 8 1_555 B C 13 1_555 0.395 0.170 0.226 4.498 -2.120 9.623 13 B_G86:C90_B B 86 ? B 90 ? 19 1 1 B G 9 1_555 B A 12 1_555 6.852 -2.203 -0.330 -3.503 -2.005 3.066 14 B_G87:A89A_B B 87 ? B 89 A ? ? # 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 U 2 1_555 A G 19 1_555 A G 4 1_555 A C 17 1_555 -2.173 -5.329 -1.832 102.727 -106.420 83.663 -2.944 0.897 0.452 -56.942 -54.966 156.232 1 AA_U80G82:C94G96_AA A 80 ? A 96 ? A 82 ? A 94 ? 1 A G 4 1_555 A C 17 1_555 A G 5 1_555 A C 16 1_555 -1.431 -3.135 3.009 -2.179 21.873 48.041 -4.600 1.510 1.595 25.380 2.528 52.558 2 AA_G82G83:C93C94_AA A 82 ? A 94 ? A 83 ? A 93 ? 1 A G 5 1_555 A C 16 1_555 A C 6 1_555 A G 15 1_555 -1.358 -2.416 2.696 -17.895 1.260 38.215 -3.483 0.209 2.944 1.809 25.680 42.073 3 AA_G83C84:G92C93_AA A 83 ? A 93 ? A 84 ? A 92 ? 1 A C 6 1_555 A G 15 1_555 A G 7 1_555 A C 14 1_555 0.561 -2.796 3.292 -2.938 5.531 19.795 -9.867 -2.676 2.326 15.592 8.282 20.753 4 AA_C84G85:C91G92_AA A 84 ? A 92 ? A 85 ? A 91 ? 1 A G 7 1_555 A C 14 1_555 A G 8 1_555 A C 13 1_555 0.803 -2.448 3.686 -4.666 6.547 47.419 -3.556 -1.378 3.252 8.073 5.754 48.057 5 AA_G85G86:C90C91_AA A 85 ? A 91 ? A 86 ? A 90 ? 1 A G 8 1_555 A C 13 1_555 A G 9 1_555 B G 20 1_555 2.570 2.911 4.376 -9.794 -19.772 -21.130 1.735 1.287 5.739 41.900 -20.756 -30.459 6 AA_G86G87:G97C90_BA A 86 ? A 90 ? A 87 ? B 97 ? 1 A G 9 1_555 B G 20 1_555 B U 2 1_555 B G 19 1_555 -2.652 5.611 3.079 -1.428 -8.028 -151.970 -2.863 -1.371 3.169 4.137 -0.736 -152.043 7 AB_G87U80:G96G97_BB A 87 ? B 97 ? B 80 ? B 96 ? 1 B U 2 1_555 B G 19 1_555 B G 4 1_555 B C 17 1_555 0.120 -3.236 5.780 -14.419 9.395 36.822 -6.412 -2.842 4.506 13.976 21.448 40.519 8 BB_U80G82:C94G96_BB B 80 ? B 96 ? B 82 ? B 94 ? 1 B G 4 1_555 B C 17 1_555 B G 5 1_555 B C 16 1_555 -1.401 -3.151 3.089 -5.429 22.881 48.406 -4.614 1.292 1.680 26.191 6.214 53.505 9 BB_G82G83:C93C94_BB B 82 ? B 94 ? B 83 ? B 93 ? 1 B G 5 1_555 B C 16 1_555 B C 6 1_555 B G 15 1_555 -1.399 -2.298 2.627 -13.814 -2.944 38.956 -2.970 0.644 3.088 -4.248 19.935 41.344 10 BB_G83C84:G92C93_BB B 83 ? B 93 ? B 84 ? B 92 ? 1 B C 6 1_555 B G 15 1_555 B G 7 1_555 B C 14 1_555 0.687 -2.821 3.198 -4.722 6.767 19.588 -9.928 -3.450 1.911 18.844 13.149 21.240 11 BB_C84G85:C91G92_BB B 84 ? B 92 ? B 85 ? B 91 ? 1 B G 7 1_555 B C 14 1_555 B G 8 1_555 B C 13 1_555 0.967 -2.427 3.936 -1.881 5.916 47.740 -3.513 -1.356 3.590 7.273 2.313 48.118 12 BB_G85G86:C90C91_BB B 85 ? B 91 ? B 86 ? B 90 ? 1 B G 8 1_555 B C 13 1_555 B G 9 1_555 B A 12 1_555 -0.726 -0.019 3.807 0.518 -11.413 56.339 0.704 0.789 3.740 -11.951 -0.543 57.392 13 BB_G86G87:A89AC90_BB B 86 ? B 90 ? B 87 ? B 89 A # _pdbx_initial_refinement_model.accession_code 5SRN _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details '16NT FRAGMENT OF DOMAINA FROM 5SRNA' # _atom_sites.entry_id 361D _atom_sites.fract_transf_matrix[1][1] 0.023430 _atom_sites.fract_transf_matrix[1][2] 0.013527 _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] 0.027055 _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] 0.006203 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_