data_4P3S # _entry.id 4P3S # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 4P3S pdb_00004p3s 10.2210/pdb4p3s/pdb WWPDB D_1000200645 ? ? # 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 2016-05-04 2 'Structure model' 1 1 2023-12-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' diffrn_source 5 2 'Structure model' pdbx_struct_oper_list # 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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 2 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 4P3S _pdbx_database_status.recvd_initial_deposition_date 2014-03-10 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs . _pdbx_database_status.methods_development_category . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 4P20 PDB . unspecified 4P3T PDB . unspecified 4P3U PDB . unspecified 4P43 PDB . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Koganei, M.' 2 # _citation.abstract . _citation.abstract_id_CAS . _citation.book_id_ISBN . _citation.book_publisher . _citation.book_publisher_city . _citation.book_title . _citation.coordinate_linkage . _citation.country ? _citation.database_id_Medline . _citation.details . _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full . _citation.journal_issue . _citation.journal_volume . _citation.language . _citation.page_first . _citation.page_last . _citation.title 'Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin' _citation.year . _citation.database_id_CSD . _citation.pdbx_database_id_DOI . _citation.pdbx_database_id_PubMed . _citation.unpublished_flag . # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Koganei, M.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'" 7410.280 2 ? ? ? ? 2 non-polymer syn GENETICIN 496.552 3 ? ? ? ? 3 water nat water 18.015 138 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'UUGCGUCCCG(5BU)CGACGAAGUCGC' _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCCCGUCGACGAAGUCGC _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 GENETICIN GET 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 U n 1 3 G n 1 4 C n 1 5 G n 1 6 U n 1 7 C n 1 8 C n 1 9 C n 1 10 G n 1 11 5BU n 1 12 C n 1 13 G n 1 14 A n 1 15 C n 1 16 G n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 23 _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id '32630 ' _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GET non-polymer . GENETICIN G418 'C20 H40 N4 O10' 496.552 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 U 1 1 ? ? ? A . n A 1 2 U 2 2 ? ? ? A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 C 8 8 8 C C A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 5BU 11 11 11 5BU 5BU A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n A 1 14 A 14 14 14 A A A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n B 1 1 U 1 24 ? ? ? B . n B 1 2 U 2 25 25 U U B . n B 1 3 G 3 26 26 G G B . n B 1 4 C 4 27 27 C C B . n B 1 5 G 5 28 28 G G B . n B 1 6 U 6 29 29 U U B . n B 1 7 C 7 30 30 C C B . n B 1 8 C 8 31 31 C C B . n B 1 9 C 9 32 32 C C B . n B 1 10 G 10 33 33 G G B . n B 1 11 5BU 11 34 34 5BU 5BU B . n B 1 12 C 12 35 35 C C B . n B 1 13 G 13 36 36 G G B . n B 1 14 A 14 37 37 A A B . n B 1 15 C 15 38 38 C C B . n B 1 16 G 16 39 39 G G B . n B 1 17 A 17 40 40 A A B . n B 1 18 A 18 41 41 A A B . n B 1 19 G 19 42 42 G G B . n B 1 20 U 20 43 43 U U B . n B 1 21 C 21 44 44 C C B . n B 1 22 G 22 45 45 G G B . n B 1 23 C 23 46 46 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 GET 1 101 50 GET GET A . D 2 GET 1 102 51 GET GET A . E 2 GET 1 103 52 GET GET A . F 3 HOH 1 201 117 HOH HOH A . F 3 HOH 2 202 236 HOH HOH A . F 3 HOH 3 203 146 HOH HOH A . F 3 HOH 4 204 127 HOH HOH A . F 3 HOH 5 205 104 HOH HOH A . F 3 HOH 6 206 139 HOH HOH A . F 3 HOH 7 207 129 HOH HOH A . F 3 HOH 8 208 125 HOH HOH A . F 3 HOH 9 209 110 HOH HOH A . F 3 HOH 10 210 186 HOH HOH A . F 3 HOH 11 211 179 HOH HOH A . F 3 HOH 12 212 108 HOH HOH A . F 3 HOH 13 213 102 HOH HOH A . F 3 HOH 14 214 142 HOH HOH A . F 3 HOH 15 215 219 HOH HOH A . F 3 HOH 16 216 234 HOH HOH A . F 3 HOH 17 217 211 HOH HOH A . F 3 HOH 18 218 137 HOH HOH A . F 3 HOH 19 219 224 HOH HOH A . F 3 HOH 20 220 159 HOH HOH A . F 3 HOH 21 221 163 HOH HOH A . F 3 HOH 22 222 120 HOH HOH A . F 3 HOH 23 223 172 HOH HOH A . F 3 HOH 24 224 207 HOH HOH A . F 3 HOH 25 225 187 HOH HOH A . F 3 HOH 26 226 158 HOH HOH A . F 3 HOH 27 227 221 HOH HOH A . F 3 HOH 28 228 227 HOH HOH A . F 3 HOH 29 229 232 HOH HOH A . F 3 HOH 30 230 208 HOH HOH A . F 3 HOH 31 231 103 HOH HOH A . F 3 HOH 32 232 113 HOH HOH A . F 3 HOH 33 233 114 HOH HOH A . F 3 HOH 34 234 115 HOH HOH A . F 3 HOH 35 235 116 HOH HOH A . F 3 HOH 36 236 121 HOH HOH A . F 3 HOH 37 237 123 HOH HOH A . F 3 HOH 38 238 131 HOH HOH A . F 3 HOH 39 239 133 HOH HOH A . F 3 HOH 40 240 143 HOH HOH A . F 3 HOH 41 241 144 HOH HOH A . F 3 HOH 42 242 147 HOH HOH A . F 3 HOH 43 243 151 HOH HOH A . F 3 HOH 44 244 155 HOH HOH A . F 3 HOH 45 245 157 HOH HOH A . F 3 HOH 46 246 165 HOH HOH A . F 3 HOH 47 247 166 HOH HOH A . F 3 HOH 48 248 168 HOH HOH A . F 3 HOH 49 249 171 HOH HOH A . F 3 HOH 50 250 173 HOH HOH A . F 3 HOH 51 251 175 HOH HOH A . F 3 HOH 52 252 176 HOH HOH A . F 3 HOH 53 253 177 HOH HOH A . F 3 HOH 54 254 178 HOH HOH A . F 3 HOH 55 255 180 HOH HOH A . F 3 HOH 56 256 182 HOH HOH A . F 3 HOH 57 257 184 HOH HOH A . F 3 HOH 58 258 185 HOH HOH A . F 3 HOH 59 259 189 HOH HOH A . F 3 HOH 60 260 190 HOH HOH A . F 3 HOH 61 261 191 HOH HOH A . F 3 HOH 62 262 192 HOH HOH A . F 3 HOH 63 263 194 HOH HOH A . F 3 HOH 64 264 195 HOH HOH A . F 3 HOH 65 265 196 HOH HOH A . F 3 HOH 66 266 202 HOH HOH A . F 3 HOH 67 267 203 HOH HOH A . F 3 HOH 68 268 213 HOH HOH A . F 3 HOH 69 269 225 HOH HOH A . F 3 HOH 70 270 226 HOH HOH A . F 3 HOH 71 271 229 HOH HOH A . F 3 HOH 72 272 230 HOH HOH A . G 3 HOH 1 101 101 HOH HOH B . G 3 HOH 2 102 118 HOH HOH B . G 3 HOH 3 103 217 HOH HOH B . G 3 HOH 4 104 188 HOH HOH B . G 3 HOH 5 105 140 HOH HOH B . G 3 HOH 6 106 135 HOH HOH B . G 3 HOH 7 107 109 HOH HOH B . G 3 HOH 8 108 122 HOH HOH B . G 3 HOH 9 109 210 HOH HOH B . G 3 HOH 10 110 112 HOH HOH B . G 3 HOH 11 111 216 HOH HOH B . G 3 HOH 12 112 106 HOH HOH B . G 3 HOH 13 113 233 HOH HOH B . G 3 HOH 14 114 231 HOH HOH B . G 3 HOH 15 115 220 HOH HOH B . G 3 HOH 16 116 128 HOH HOH B . G 3 HOH 17 117 237 HOH HOH B . G 3 HOH 18 118 160 HOH HOH B . G 3 HOH 19 119 212 HOH HOH B . G 3 HOH 20 120 204 HOH HOH B . G 3 HOH 21 121 209 HOH HOH B . G 3 HOH 22 122 154 HOH HOH B . G 3 HOH 23 123 161 HOH HOH B . G 3 HOH 24 124 153 HOH HOH B . G 3 HOH 25 125 162 HOH HOH B . G 3 HOH 26 126 206 HOH HOH B . G 3 HOH 27 127 201 HOH HOH B . G 3 HOH 28 128 200 HOH HOH B . G 3 HOH 29 129 105 HOH HOH B . G 3 HOH 30 130 107 HOH HOH B . G 3 HOH 31 131 111 HOH HOH B . G 3 HOH 32 132 119 HOH HOH B . G 3 HOH 33 133 124 HOH HOH B . G 3 HOH 34 134 126 HOH HOH B . G 3 HOH 35 135 130 HOH HOH B . G 3 HOH 36 136 132 HOH HOH B . G 3 HOH 37 137 134 HOH HOH B . G 3 HOH 38 138 136 HOH HOH B . G 3 HOH 39 139 138 HOH HOH B . G 3 HOH 40 140 141 HOH HOH B . G 3 HOH 41 141 145 HOH HOH B . G 3 HOH 42 142 148 HOH HOH B . G 3 HOH 43 143 149 HOH HOH B . G 3 HOH 44 144 150 HOH HOH B . G 3 HOH 45 145 152 HOH HOH B . G 3 HOH 46 146 156 HOH HOH B . G 3 HOH 47 147 164 HOH HOH B . G 3 HOH 48 148 167 HOH HOH B . G 3 HOH 49 149 169 HOH HOH B . G 3 HOH 50 150 170 HOH HOH B . G 3 HOH 51 151 174 HOH HOH B . G 3 HOH 52 152 181 HOH HOH B . G 3 HOH 53 153 183 HOH HOH B . G 3 HOH 54 154 193 HOH HOH B . G 3 HOH 55 155 197 HOH HOH B . G 3 HOH 56 156 198 HOH HOH B . G 3 HOH 57 157 199 HOH HOH B . G 3 HOH 58 158 205 HOH HOH B . G 3 HOH 59 159 214 HOH HOH B . G 3 HOH 60 160 215 HOH HOH B . G 3 HOH 61 161 218 HOH HOH B . G 3 HOH 62 162 222 HOH HOH B . G 3 HOH 63 163 223 HOH HOH B . G 3 HOH 64 164 228 HOH HOH B . G 3 HOH 65 165 235 HOH HOH B . G 3 HOH 66 166 238 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data collection' . . . . . . . . . . . CrystalClear . . . . 1 ? phasing . . . . . . . . . . . PHENIX . . . . 2 ? refinement . . . . . . . . . . . CNS . . . . 3 ? 'data extraction' . . . . . . . . . . . PDB_EXTRACT . . . 3.14 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? SOLVE ? ? ? . 5 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? d*TREK ? ? ? . 6 # _cell.length_a 34.090 _cell.length_b 88.830 _cell.length_c 46.610 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 4P3S _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P3S _symmetry.cell_setting . _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M . # _exptl.absorpt_coefficient_mu . _exptl.absorpt_correction_T_max . _exptl.absorpt_correction_T_min . _exptl.absorpt_correction_type . _exptl.absorpt_process_details . _exptl.entry_id 4P3S _exptl.crystals_number 1 _exptl.details . _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details . # _exptl_crystal.colour . _exptl_crystal.density_diffrn . _exptl_crystal.density_Matthews 2.41 _exptl_crystal.density_method . _exptl_crystal.density_percent_sol 48.89 _exptl_crystal.description . _exptl_crystal.F_000 . _exptl_crystal.id 1 _exptl_crystal.preparation . _exptl_crystal.size_max . _exptl_crystal.size_mid . _exptl_crystal.size_min . _exptl_crystal.size_rad . _exptl_crystal.colour_lustre . _exptl_crystal.colour_modifier . _exptl_crystal.colour_primary . _exptl_crystal.density_meas . _exptl_crystal.density_meas_esd . _exptl_crystal.density_meas_gt . _exptl_crystal.density_meas_lt . _exptl_crystal.density_meas_temp . _exptl_crystal.density_meas_temp_esd . _exptl_crystal.density_meas_temp_gt . _exptl_crystal.density_meas_temp_lt . _exptl_crystal.pdbx_crystal_image_url . _exptl_crystal.pdbx_crystal_image_format . _exptl_crystal.pdbx_mosaicity . _exptl_crystal.pdbx_mosaicity_esd . # _exptl_crystal_grow.apparatus . _exptl_crystal_grow.atmosphere . _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details . _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref . _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pressure . _exptl_crystal_grow.pressure_esd . _exptl_crystal_grow.seeding . _exptl_crystal_grow.seeding_ref . _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details . _exptl_crystal_grow.temp_esd . _exptl_crystal_grow.time . _exptl_crystal_grow.pdbx_details 'Sodium Cacodylate (pH7), Spermine tetrahydrochloride, MPD, Sodium Chloride' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.ambient_environment . _diffrn.ambient_temp 100 _diffrn.ambient_temp_details . _diffrn.ambient_temp_esd . _diffrn.crystal_id 1 _diffrn.crystal_support . _diffrn.crystal_treatment . _diffrn.details . _diffrn.id 1 _diffrn.ambient_pressure . _diffrn.ambient_pressure_esd . _diffrn.ambient_pressure_gt . _diffrn.ambient_pressure_lt . _diffrn.ambient_temp_gt . _diffrn.ambient_temp_lt . # _diffrn_detector.details . _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 210r' _diffrn_detector.area_resol_mean . _diffrn_detector.dtime . _diffrn_detector.pdbx_frames_total . _diffrn_detector.pdbx_collection_time_total . _diffrn_detector.pdbx_collection_date 2012-12-11 # _diffrn_radiation.collimation . _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge . _diffrn_radiation.inhomogeneity . _diffrn_radiation.monochromator . _diffrn_radiation.polarisn_norm . _diffrn_radiation.polarisn_ratio . _diffrn_radiation.probe . _diffrn_radiation.type . _diffrn_radiation.xray_symbol . _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list . _diffrn_radiation.pdbx_wavelength . _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_analyzer . _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91938 1.0 2 0.92004 1.0 3 0.90659 1.0 4 1.0 1.0 # _diffrn_source.current . _diffrn_source.details . _diffrn_source.diffrn_id 1 _diffrn_source.power . _diffrn_source.size . _diffrn_source.source SYNCHROTRON _diffrn_source.target . _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-5A' _diffrn_source.voltage . _diffrn_source.take-off_angle . _diffrn_source.pdbx_wavelength_list '0.91938, 0.92004, 0.90659, 1.0' _diffrn_source.pdbx_wavelength . _diffrn_source.pdbx_synchrotron_beamline BL-5A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate . _reflns.entry_id 4P3S _reflns.data_reduction_details . _reflns.data_reduction_method . _reflns.d_resolution_high 2.300 _reflns.d_resolution_low 44.420 _reflns.details . _reflns.limit_h_max . _reflns.limit_h_min . _reflns.limit_k_max . _reflns.limit_k_min . _reflns.limit_l_max . _reflns.limit_l_min . _reflns.number_all . _reflns.number_obs 6694 _reflns.observed_criterion . _reflns.observed_criterion_F_max . _reflns.observed_criterion_F_min . _reflns.observed_criterion_I_max . _reflns.observed_criterion_I_min . _reflns.observed_criterion_sigma_F . _reflns.observed_criterion_sigma_I . _reflns.percent_possible_obs 99.700 _reflns.R_free_details . _reflns.Rmerge_F_all . _reflns.Rmerge_F_obs . _reflns.Friedel_coverage . _reflns.number_gt . _reflns.threshold_expression . _reflns.pdbx_redundancy 6.720 _reflns.pdbx_Rmerge_I_obs 0.050 _reflns.pdbx_Rmerge_I_all . _reflns.pdbx_Rsym_value . _reflns.pdbx_netI_over_av_sigmaI . _reflns.pdbx_netI_over_sigmaI 17.600 _reflns.pdbx_res_netI_over_av_sigmaI_2 . _reflns.pdbx_res_netI_over_sigmaI_2 . _reflns.pdbx_chi_squared 0.940 _reflns.pdbx_scaling_rejects 340 _reflns.pdbx_d_res_high_opt . _reflns.pdbx_d_res_low_opt . _reflns.pdbx_d_res_opt_method . _reflns.phase_calculation_details . _reflns.pdbx_Rrim_I_all . _reflns.pdbx_Rpim_I_all . _reflns.pdbx_d_opt . _reflns.pdbx_number_measured_all 45316 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.300 2.380 . 4.400 4663 . . 659 . 100.000 . . . . 0.347 . . . . . . . . 7.040 . 1.180 . . . . 21 1 1 2.380 2.480 . 4.400 4492 . . 651 . 100.000 . . . . 0.324 . . . . . . . . 6.880 . 1.100 . . . . 10 2 1 2.480 2.590 . 6.200 4646 . . 660 . 100.000 . . . . 0.227 . . . . . . . . 6.990 . 1.050 . . . . 31 3 1 2.590 2.730 . 7.400 4452 . . 649 . 100.000 . . . . 0.192 . . . . . . . . 6.760 . 1.180 . . . . 63 4 1 2.730 2.900 . 10.300 4558 . . 657 . 100.000 . . . . 0.123 . . . . . . . . 6.920 . 0.960 . . . . 14 5 1 2.900 3.120 . 15.600 4669 . . 674 . 100.000 . . . . 0.076 . . . . . . . . 6.890 . 0.860 . . . . 23 6 1 3.120 3.440 . 23.700 4524 . . 663 . 99.700 . . . . 0.046 . . . . . . . . 6.770 . 0.850 . . . . 37 7 1 3.440 3.930 . 26.800 4438 . . 670 . 99.600 . . . . 0.042 . . . . . . . . 6.510 . 0.770 . . . . 77 8 1 3.930 4.950 . 30.300 4438 . . 687 . 100.000 . . . . 0.038 . . . . . . . . 6.450 . 0.710 . . . . 10 9 1 4.950 44.420 . 49.200 4436 . . 724 . 97.600 . . . . 0.023 . . . . . . . . 6.050 . 0.740 . . . . 54 10 1 # _refine.aniso_B[1][1] 0.4780 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][2] 7.4520 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] -7.9300 _refine.B_iso_max 99.240 _refine.B_iso_mean 39.1932 _refine.B_iso_min 19.010 _refine.correlation_coeff_Fo_to_Fc . _refine.correlation_coeff_Fo_to_Fc_free . _refine.details . _refine.diff_density_max . _refine.diff_density_max_esd . _refine.diff_density_min . _refine.diff_density_min_esd . _refine.diff_density_rms . _refine.diff_density_rms_esd . _refine.entry_id 4P3S _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details . _refine.ls_abs_structure_Flack . _refine.ls_abs_structure_Flack_esd . _refine.ls_abs_structure_Rogers . _refine.ls_abs_structure_Rogers_esd . _refine.ls_d_res_high 2.3000 _refine.ls_d_res_low 100.0000 _refine.ls_extinction_coef . _refine.ls_extinction_coef_esd . _refine.ls_extinction_expression . _refine.ls_extinction_method . _refine.ls_goodness_of_fit_all . _refine.ls_goodness_of_fit_all_esd . _refine.ls_goodness_of_fit_obs . _refine.ls_goodness_of_fit_obs_esd . _refine.ls_hydrogen_treatment . _refine.ls_matrix_type . _refine.ls_number_constraints . _refine.ls_number_parameters . _refine.ls_number_reflns_all . _refine.ls_number_reflns_obs 6694 _refine.ls_number_reflns_R_free 726 _refine.ls_number_reflns_R_work 5968 _refine.ls_number_restraints . _refine.ls_percent_reflns_obs 99.6000 _refine.ls_percent_reflns_R_free 10.8000 _refine.ls_R_factor_all . _refine.ls_R_factor_obs . _refine.ls_R_factor_R_free 0.2646 _refine.ls_R_factor_R_free_error . _refine.ls_R_factor_R_free_error_details . _refine.ls_R_factor_R_work 0.2194 _refine.ls_R_Fsqd_factor_obs . _refine.ls_R_I_factor_obs . _refine.ls_redundancy_reflns_all . _refine.ls_redundancy_reflns_obs . _refine.ls_restrained_S_all . _refine.ls_restrained_S_obs . _refine.ls_shift_over_esd_max . _refine.ls_shift_over_esd_mean . _refine.ls_structure_factor_coef . _refine.ls_weighting_details . _refine.ls_weighting_scheme . _refine.ls_wR_factor_all . _refine.ls_wR_factor_obs . _refine.ls_wR_factor_R_free . _refine.ls_wR_factor_R_work . _refine.occupancy_max . _refine.occupancy_min . _refine.overall_SU_B . _refine.overall_SU_ML . _refine.overall_SU_R_Cruickshank_DPI . _refine.overall_SU_R_free . _refine.overall_FOM_free_R_set . _refine.overall_FOM_work_R_set 0.7962 _refine.solvent_model_details . _refine.solvent_model_param_bsol 65.1243 _refine.solvent_model_param_ksol . _refine.ls_R_factor_gt . _refine.ls_goodness_of_fit_gt . _refine.ls_goodness_of_fit_ref . _refine.ls_shift_over_su_max . _refine.ls_shift_over_su_max_lt . _refine.ls_shift_over_su_mean . _refine.ls_shift_over_su_mean_lt . _refine.pdbx_ls_sigma_I . _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_ls_sigma_Fsqd . _refine.pdbx_data_cutoff_high_absF . _refine.pdbx_data_cutoff_high_rms_absF . _refine.pdbx_data_cutoff_low_absF . _refine.pdbx_isotropic_thermal_model . _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model . _refine.pdbx_stereochemistry_target_values . _refine.pdbx_R_Free_selection_details . _refine.pdbx_stereochem_target_val_spec_case . _refine.pdbx_overall_ESU_R . _refine.pdbx_overall_ESU_R_Free . _refine.pdbx_solvent_vdw_probe_radii . _refine.pdbx_solvent_ion_probe_radii . _refine.pdbx_solvent_shrinkage_radii . _refine.pdbx_real_space_R . _refine.pdbx_density_correlation . _refine.pdbx_pd_number_of_powder_patterns . _refine.pdbx_pd_number_of_points . _refine.pdbx_pd_meas_number_of_points . _refine.pdbx_pd_proc_ls_prof_R_factor . _refine.pdbx_pd_proc_ls_prof_wR_factor . _refine.pdbx_pd_Marquardt_correlation_coeff . _refine.pdbx_pd_Fsqrd_R_factor . _refine.pdbx_pd_ls_matrix_band_width . _refine.pdbx_overall_phase_error . _refine.pdbx_overall_SU_R_free_Cruickshank_DPI . _refine.pdbx_overall_SU_R_free_Blow_DPI . _refine.pdbx_overall_SU_R_Blow_DPI . _refine.pdbx_TLS_residual_ADP_flag . _refine.pdbx_diffrn_id 1 # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 2.3000 _refine_hist.d_res_low 100.0000 _refine_hist.pdbx_number_atoms_ligand 102 _refine_hist.number_atoms_solvent 138 _refine_hist.number_atoms_total 1156 _refine_hist.pdbx_number_residues_total 43 _refine_hist.pdbx_B_iso_mean_ligand 45.54 _refine_hist.pdbx_B_iso_mean_solvent 46.94 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 916 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' . 0.006 . . . c_bond_d . . 'X-RAY DIFFRACTION' . 0.910 . . . c_angle_d . . 'X-RAY DIFFRACTION' . 0.000 1.500 . . c_mcbond_it . . 'X-RAY DIFFRACTION' . 1.717 2.000 . . c_scbond_it . . 'X-RAY DIFFRACTION' . 0.000 2.000 . . c_mcangle_it . . 'X-RAY DIFFRACTION' . 2.442 2.500 . . c_scangle_it . . # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error 'X-RAY DIFFRACTION' 2.3000 2.3800 656 . 67 589 100.0000 . . . 0.4083 . 0.3967 . . . . . . 10 . 'X-RAY DIFFRACTION' 2.3800 2.4800 650 . 84 566 100.0000 . . . 0.5019 . 0.4463 . . . . . . 10 . 'X-RAY DIFFRACTION' 2.4800 2.5900 663 . 66 597 100.0000 . . . 0.4026 . 0.3508 . . . . . . 10 . 'X-RAY DIFFRACTION' 2.5900 2.7300 647 . 67 580 100.0000 . . . 0.3122 . 0.3121 . . . . . . 10 . 'X-RAY DIFFRACTION' 2.7300 2.9000 660 . 60 600 100.0000 . . . 0.3791 . 0.3008 . . . . . . 10 . 'X-RAY DIFFRACTION' 2.9000 3.1200 669 . 86 583 100.0000 . . . 0.3026 . 0.2213 . . . . . . 10 . 'X-RAY DIFFRACTION' 3.1200 3.4400 668 . 70 598 99.7000 . . . 0.2478 . 0.2099 . . . . . . 10 . 'X-RAY DIFFRACTION' 3.4400 3.9300 670 . 77 593 99.6000 . . . 0.2233 . 0.1821 . . . . . . 10 . 'X-RAY DIFFRACTION' 3.9300 4.9600 687 . 75 612 100.0000 . . . 0.2207 . 0.1545 . . . . . . 10 . 'X-RAY DIFFRACTION' 4.9600 100.0000 724 . 74 650 97.3000 . . . 0.2057 . 0.1904 . . . . . . 10 . # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 dna-rna_free.param ? 'X-RAY DIFFRACTION' 2 CNS_TOPPAR:water_rep.param ? 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:ion.param ? 'X-RAY DIFFRACTION' 4 bru.param ? 'X-RAY DIFFRACTION' 5 get_xplor.param ? # _struct.entry_id 4P3S _struct.title 'Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin' _struct.pdbx_model_details . _struct.pdbx_formula_weight . _struct.pdbx_formula_weight_method . _struct.pdbx_model_type_details . _struct.pdbx_CASP_flag . # _struct_keywords.entry_id 4P3S _struct_keywords.text 'ribosome, antibiotic-resistance, aminoglycoside, decoding, RNA-ANTIBIOTIC complex' _struct_keywords.pdbx_keywords RNA/ANTIBIOTIC # 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 ? E N N 2 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4P3S _struct_ref.pdbx_db_accession 4P3S _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _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 4P3S A 1 ? 23 ? 4P3S 1 ? 23 ? 1 23 2 1 4P3S B 1 ? 23 ? 4P3S 24 ? 46 ? 24 46 # _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)' 4460 ? 1 MORE -62 ? 1 'SSA (A^2)' 8150 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 10 "O3'" ? ? ? 1_555 A 5BU 11 P ? ? A G 10 A 5BU 11 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale2 covale both ? A 5BU 11 "O3'" ? ? ? 1_555 A C 12 P ? ? A 5BU 11 A C 12 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale3 covale both ? B G 10 "O3'" ? ? ? 1_555 B 5BU 11 P ? ? B G 33 B 5BU 34 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale both ? B 5BU 11 "O3'" ? ? ? 1_555 B C 12 P ? ? B 5BU 34 B C 35 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 6 O4 ? ? ? 1_555 B U 20 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A 5BU 11 N3 ? ? ? 1_555 B A 14 N1 ? ? A 5BU 11 B A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A 5BU 11 O4 ? ? ? 1_555 B A 14 N6 ? ? A 5BU 11 B A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 14 N1 ? ? ? 1_555 B 5BU 11 N3 ? ? A A 14 B 5BU 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 14 N6 ? ? ? 1_555 B 5BU 11 O4 ? ? A A 14 B 5BU 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 16 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 16 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 16 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O4 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog40 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 GET 101 ? 17 'binding site for residue GET A 101' AC2 Software A GET 102 ? 16 'binding site for residue GET A 102' AC3 Software A GET 103 ? 10 'binding site for residue GET A 103' # 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 17 C A 4 ? C A 4 . ? 1_555 ? 2 AC1 17 G A 5 ? G A 5 . ? 1_555 ? 3 AC1 17 U A 6 ? U A 6 . ? 1_555 ? 4 AC1 17 C A 7 ? C A 7 . ? 1_555 ? 5 AC1 17 C A 8 ? C A 8 . ? 1_555 ? 6 AC1 17 C A 9 ? C A 9 . ? 1_555 ? 7 AC1 17 HOH F . ? HOH A 208 . ? 1_555 ? 8 AC1 17 HOH F . ? HOH A 251 . ? 1_555 ? 9 AC1 17 HOH F . ? HOH A 264 . ? 1_555 ? 10 AC1 17 HOH F . ? HOH A 265 . ? 1_555 ? 11 AC1 17 G B 16 ? G B 39 . ? 1_555 ? 12 AC1 17 A B 17 ? A B 40 . ? 1_555 ? 13 AC1 17 A B 18 ? A B 41 . ? 1_555 ? 14 AC1 17 G B 19 ? G B 42 . ? 1_555 ? 15 AC1 17 U B 20 ? U B 43 . ? 1_555 ? 16 AC1 17 HOH G . ? HOH B 105 . ? 1_555 ? 17 AC1 17 HOH G . ? HOH B 136 . ? 1_555 ? 18 AC2 16 G A 16 ? G A 16 . ? 1_555 ? 19 AC2 16 A A 17 ? A A 17 . ? 1_555 ? 20 AC2 16 A A 18 ? A A 18 . ? 1_555 ? 21 AC2 16 G A 19 ? G A 19 . ? 1_555 ? 22 AC2 16 U A 20 ? U A 20 . ? 1_555 ? 23 AC2 16 HOH F . ? HOH A 231 . ? 1_555 ? 24 AC2 16 HOH F . ? HOH A 235 . ? 1_555 ? 25 AC2 16 HOH F . ? HOH A 236 . ? 1_555 ? 26 AC2 16 HOH F . ? HOH A 241 . ? 1_555 ? 27 AC2 16 HOH F . ? HOH A 259 . ? 1_555 ? 28 AC2 16 C B 4 ? C B 27 . ? 1_555 ? 29 AC2 16 G B 5 ? G B 28 . ? 1_555 ? 30 AC2 16 U B 6 ? U B 29 . ? 1_555 ? 31 AC2 16 C B 7 ? C B 30 . ? 1_555 ? 32 AC2 16 C B 8 ? C B 31 . ? 1_555 ? 33 AC2 16 C B 9 ? C B 32 . ? 1_555 ? 34 AC3 10 U A 6 ? U A 6 . ? 1_555 ? 35 AC3 10 C A 7 ? C A 7 . ? 1_555 ? 36 AC3 10 C A 8 ? C A 8 . ? 1_555 ? 37 AC3 10 HOH F . ? HOH A 237 . ? 1_555 ? 38 AC3 10 HOH F . ? HOH A 240 . ? 1_555 ? 39 AC3 10 HOH F . ? HOH A 244 . ? 1_555 ? 40 AC3 10 HOH F . ? HOH A 263 . ? 1_555 ? 41 AC3 10 C B 12 ? C B 35 . ? 1_555 ? 42 AC3 10 G B 13 ? G B 36 . ? 1_555 ? 43 AC3 10 HOH G . ? HOH B 129 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 C71 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 GET _pdbx_validate_close_contact.auth_seq_id_1 103 _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 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 244 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.08 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 226 ? F HOH . 2 1 A HOH 266 ? F HOH . 3 1 B HOH 124 ? G HOH . # _phasing.method MAD # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id A _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 266 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.61 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 1 ? A U 1 2 1 Y 1 A U 2 ? A U 2 3 1 Y 1 B U 24 ? B U 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 GET C11 C N S 145 GET O11 O N N 146 GET C21 C N R 147 GET N21 N N N 148 GET C31 C N R 149 GET O31 O N N 150 GET C41 C N S 151 GET O41 O N N 152 GET C51 C N R 153 GET O51 O N N 154 GET C61 C N R 155 GET O61 O N N 156 GET C71 C N N 157 GET C12 C N R 158 GET N12 N N N 159 GET C22 C N N 160 GET C32 C N S 161 GET N32 N N N 162 GET C42 C N R 163 GET C52 C N S 164 GET O52 O N N 165 GET C62 C N S 166 GET O62 O N N 167 GET C13 C N R 168 GET C23 C N R 169 GET O23 O N N 170 GET C33 C N R 171 GET N33 N N N 172 GET C93 C N N 173 GET C43 C N R 174 GET O43 O N N 175 GET C83 C N N 176 GET C53 C N N 177 GET O53 O N N 178 GET H111 H N N 179 GET H21 H N N 180 GET H211 H N N 181 GET H212 H N N 182 GET H311 H N N 183 GET H31 H N N 184 GET H411 H N N 185 GET H41 H N N 186 GET H511 H N N 187 GET H611 H N N 188 GET H61 H N N 189 GET H711 H N N 190 GET H712 H N N 191 GET H713 H N N 192 GET H12 H N N 193 GET H121 H N N 194 GET H122 H N N 195 GET H221 H N N 196 GET H222 H N N 197 GET H32 H N N 198 GET H321 H N N 199 GET H322 H N N 200 GET H421 H N N 201 GET H521 H N N 202 GET H52 H N N 203 GET H621 H N N 204 GET H131 H N N 205 GET H231 H N N 206 GET H23 H N N 207 GET H331 H N N 208 GET H33 H N N 209 GET H931 H N N 210 GET H932 H N N 211 GET H933 H N N 212 GET H43 H N N 213 GET H831 H N N 214 GET H832 H N N 215 GET H833 H N N 216 GET H531 H N N 217 GET H532 H N N 218 HOH O O N N 219 HOH H1 H N N 220 HOH H2 H N N 221 U OP3 O N N 222 U P P N N 223 U OP1 O N N 224 U OP2 O N N 225 U "O5'" O N N 226 U "C5'" C N N 227 U "C4'" C N R 228 U "O4'" O N N 229 U "C3'" C N S 230 U "O3'" O N N 231 U "C2'" C N R 232 U "O2'" O N N 233 U "C1'" C N R 234 U N1 N N N 235 U C2 C N N 236 U O2 O N N 237 U N3 N N N 238 U C4 C N N 239 U O4 O N N 240 U C5 C N N 241 U C6 C N N 242 U HOP3 H N N 243 U HOP2 H N N 244 U "H5'" H N N 245 U "H5''" H N N 246 U "H4'" H N N 247 U "H3'" H N N 248 U "HO3'" H N N 249 U "H2'" H N N 250 U "HO2'" H N N 251 U "H1'" H N N 252 U H3 H N N 253 U H5 H N N 254 U H6 H N N 255 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 GET C11 O11 sing N N 151 GET C11 C21 sing N N 152 GET C11 O51 sing N N 153 GET C11 H111 sing N N 154 GET O11 C42 sing N N 155 GET C21 N21 sing N N 156 GET C21 C31 sing N N 157 GET C21 H21 sing N N 158 GET N21 H211 sing N N 159 GET N21 H212 sing N N 160 GET C31 O31 sing N N 161 GET C31 C41 sing N N 162 GET C31 H311 sing N N 163 GET O31 H31 sing N N 164 GET C41 O41 sing N N 165 GET C41 C51 sing N N 166 GET C41 H411 sing N N 167 GET O41 H41 sing N N 168 GET C51 O51 sing N N 169 GET C51 C61 sing N N 170 GET C51 H511 sing N N 171 GET C61 O61 sing N N 172 GET C61 C71 sing N N 173 GET C61 H611 sing N N 174 GET O61 H61 sing N N 175 GET C71 H711 sing N N 176 GET C71 H712 sing N N 177 GET C71 H713 sing N N 178 GET C12 N12 sing N N 179 GET C12 C22 sing N N 180 GET C12 C62 sing N N 181 GET C12 H12 sing N N 182 GET N12 H121 sing N N 183 GET N12 H122 sing N N 184 GET C22 C32 sing N N 185 GET C22 H221 sing N N 186 GET C22 H222 sing N N 187 GET C32 N32 sing N N 188 GET C32 C42 sing N N 189 GET C32 H32 sing N N 190 GET N32 H321 sing N N 191 GET N32 H322 sing N N 192 GET C42 C52 sing N N 193 GET C42 H421 sing N N 194 GET C52 O52 sing N N 195 GET C52 C62 sing N N 196 GET C52 H521 sing N N 197 GET O52 H52 sing N N 198 GET C62 O62 sing N N 199 GET C62 H621 sing N N 200 GET O62 C13 sing N N 201 GET C13 C23 sing N N 202 GET C13 O53 sing N N 203 GET C13 H131 sing N N 204 GET C23 O23 sing N N 205 GET C23 C33 sing N N 206 GET C23 H231 sing N N 207 GET O23 H23 sing N N 208 GET C33 N33 sing N N 209 GET C33 C43 sing N N 210 GET C33 H331 sing N N 211 GET N33 C93 sing N N 212 GET N33 H33 sing N N 213 GET C93 H931 sing N N 214 GET C93 H932 sing N N 215 GET C93 H933 sing N N 216 GET C43 O43 sing N N 217 GET C43 C83 sing N N 218 GET C43 C53 sing N N 219 GET O43 H43 sing N N 220 GET C83 H831 sing N N 221 GET C83 H832 sing N N 222 GET C83 H833 sing N N 223 GET C53 O53 sing N N 224 GET C53 H531 sing N N 225 GET C53 H532 sing N N 226 HOH O H1 sing N N 227 HOH O H2 sing N N 228 U OP3 P sing N N 229 U OP3 HOP3 sing N N 230 U P OP1 doub N N 231 U P OP2 sing N N 232 U P "O5'" sing N N 233 U OP2 HOP2 sing N N 234 U "O5'" "C5'" sing N N 235 U "C5'" "C4'" sing N N 236 U "C5'" "H5'" sing N N 237 U "C5'" "H5''" sing N N 238 U "C4'" "O4'" sing N N 239 U "C4'" "C3'" sing N N 240 U "C4'" "H4'" sing N N 241 U "O4'" "C1'" sing N N 242 U "C3'" "O3'" sing N N 243 U "C3'" "C2'" sing N N 244 U "C3'" "H3'" sing N N 245 U "O3'" "HO3'" sing N N 246 U "C2'" "O2'" sing N N 247 U "C2'" "C1'" sing N N 248 U "C2'" "H2'" sing N N 249 U "O2'" "HO2'" sing N N 250 U "C1'" N1 sing N N 251 U "C1'" "H1'" sing N N 252 U N1 C2 sing N N 253 U N1 C6 sing N N 254 U C2 O2 doub N N 255 U C2 N3 sing N N 256 U N3 C4 sing N N 257 U N3 H3 sing N N 258 U C4 O4 doub N N 259 U C4 C5 sing N N 260 U C5 C6 doub N N 261 U C5 H5 sing N N 262 U C6 H6 sing N N 263 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4P3S 'double helix' 4P3S 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 3 1_555 B C 23 1_555 -0.677 -0.046 0.064 -4.236 -1.318 5.399 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 4 1_555 B G 22 1_555 0.239 -0.086 0.098 6.912 -6.315 -1.748 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 5 1_555 B C 21 1_555 -0.285 -0.198 -0.397 -5.817 -9.024 3.547 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 6 1_555 B U 20 1_555 -2.360 -1.595 -0.366 14.393 -10.447 -4.381 4 A_U6:U43_B A 6 ? B 43 ? ? ? 1 A C 7 1_555 B G 19 1_555 0.148 -0.175 -0.487 4.099 -1.682 2.510 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 9 1_555 B G 16 1_555 0.327 -0.041 -0.130 6.624 -14.216 0.894 6 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A G 10 1_555 B C 15 1_555 -0.230 -0.103 0.288 -2.562 -10.087 2.109 7 A_G10:C38_B A 10 ? B 38 ? 19 1 1 A 5BU 11 1_555 B A 14 1_555 -0.261 -0.104 0.092 -2.341 -11.603 -3.047 8 A_5BU11:A37_B A 11 ? B 37 ? 20 1 1 A C 12 1_555 B G 13 1_555 0.346 -0.081 0.089 3.134 -12.921 2.415 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.180 -0.125 0.016 -0.090 -10.337 -1.014 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A A 14 1_555 B 5BU 11 1_555 0.086 -0.109 0.248 4.843 -15.631 -0.260 11 A_A14:5BU34_B A 14 ? B 34 ? 20 1 1 A C 15 1_555 B G 10 1_555 0.223 -0.027 0.101 -1.887 -15.593 6.739 12 A_C15:G33_B A 15 ? B 33 ? 19 1 1 A G 16 1_555 B C 9 1_555 -0.209 -0.145 -0.010 0.417 -7.309 2.652 13 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A G 19 1_555 B C 7 1_555 -0.133 -0.208 -0.272 4.522 8.296 -0.192 14 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B U 6 1_555 2.056 -1.475 -0.316 -7.155 -7.333 -10.339 15 A_U20:U29_B A 20 ? B 29 ? ? ? 1 A C 21 1_555 B G 5 1_555 0.065 -0.286 -0.248 0.937 -5.606 -0.681 16 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 4 1_555 -0.235 -0.284 0.267 -0.889 -10.134 -3.401 17 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.323 -0.252 0.207 -2.221 -2.281 -0.536 18 A_C23:G26_B A 23 ? B 26 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 3 1_555 B C 23 1_555 A C 4 1_555 B G 22 1_555 -1.030 -1.194 3.038 -1.967 4.039 35.718 -2.460 1.411 2.941 6.553 3.191 35.991 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 0.696 -1.601 3.577 1.680 7.338 30.778 -4.348 -0.951 3.154 13.572 -3.108 31.664 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B U 20 1_555 -0.448 -1.651 2.602 -2.688 1.081 22.942 -4.417 0.377 2.558 2.703 6.723 23.122 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 6 1_555 B U 20 1_555 A C 7 1_555 B G 19 1_555 0.702 -2.338 3.748 -1.258 5.910 42.333 -3.857 -1.101 3.386 8.133 1.732 42.743 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 9 1_555 B G 16 1_555 A G 10 1_555 B C 15 1_555 -0.347 -2.104 3.465 -6.433 11.080 27.113 -6.254 -0.594 2.454 22.133 12.850 29.936 5 AA_C9G10:C38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A G 10 1_555 B C 15 1_555 A 5BU 11 1_555 B A 14 1_555 -0.780 -1.499 3.177 -0.726 5.437 32.726 -3.481 1.252 2.913 9.566 1.277 33.170 6 AA_G105BU11:A37C38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A 5BU 11 1_555 B A 14 1_555 A C 12 1_555 B G 13 1_555 0.938 -1.477 3.154 0.347 5.114 32.959 -3.366 -1.582 2.908 8.946 -0.606 33.344 7 AA_5BU11C12:G36A37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 -0.584 -1.575 3.295 0.099 9.184 30.503 -4.448 1.082 2.716 16.978 -0.183 31.825 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 13 1_555 B C 12 1_555 A A 14 1_555 B 5BU 11 1_555 0.054 -1.368 3.090 -1.860 5.622 32.300 -3.297 -0.386 2.811 10.001 3.308 32.824 9 AA_G13A14:5BU34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A A 14 1_555 B 5BU 11 1_555 A C 15 1_555 B G 10 1_555 0.919 -1.825 3.347 3.239 3.249 32.819 -3.754 -1.060 3.229 5.716 -5.697 33.129 10 AA_A14C15:G335BU34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A C 15 1_555 B G 10 1_555 A G 16 1_555 B C 9 1_555 -0.583 -1.926 3.176 0.260 8.704 27.427 -5.601 1.225 2.456 17.797 -0.532 28.751 11 AA_C15G16:C32G33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 -1.044 -2.434 3.799 0.862 2.796 41.624 -3.752 1.569 3.614 3.929 -1.211 41.722 12 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 0.379 -2.010 2.989 1.512 1.448 25.183 -4.975 -0.469 2.888 3.315 -3.459 25.269 13 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 -0.048 -1.640 3.237 -1.751 6.863 31.236 -4.137 -0.210 2.821 12.545 3.201 32.010 14 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 0.727 -2.058 3.361 2.468 1.633 34.197 -3.750 -0.837 3.305 2.771 -4.187 34.321 15 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # _pdbx_audit_support.funding_organization MEXT _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 23790054 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 4P3S _atom_sites.fract_transf_matrix[1][1] 0.029334 _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] 0.011257 _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] 0.021455 _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 BR C N O P # loop_