data_3E5C # _entry.id 3E5C # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3E5C pdb_00003e5c 10.2210/pdb3e5c/pdb NDB UR0166 ? ? RCSB RCSB048894 ? ? WWPDB D_1000048894 ? ? # 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 2008-10-07 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_conn_type 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.conn_type_id' 4 3 'Structure model' '_struct_conn.id' 5 3 'Structure model' '_struct_conn.pdbx_dist_value' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 19 3 'Structure model' '_struct_conn_type.id' 20 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3E5C _pdbx_database_status.recvd_initial_deposition_date 2008-08-13 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3E5E . unspecified PDB 3E5F . unspecified # _audit_author.name 'Lu, C.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.' _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_volume 15 _citation.page_first 1076 _citation.page_last 1083 _citation.year 2008 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1545-9993 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18806797 _citation.pdbx_database_id_DOI 10.1038/nsmb.1494 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lu, C.' 1 ? primary 'Smith, A.M.' 2 ? primary 'Fuchs, R.T.' 3 ? primary 'Ding, F.' 4 ? primary 'Rajashankar, K.' 5 ? primary 'Henkin, T.M.' 6 ? primary 'Ke, A.' 7 ? # 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 'SMK box (SAM-III) Riboswitch' 17402.322 1 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 15 ? ? ? ? 3 non-polymer syn S-ADENOSYLMETHIONINE 398.437 1 ? ? ? ? 4 water nat water 18.015 69 ? ? ? ? # _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 '(GTP)UUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU' _entity_poly.pdbx_seq_one_letter_code_can GUUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'STRONTIUM ION' SR 3 S-ADENOSYLMETHIONINE SAM 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GTP n 1 2 U n 1 3 U n 1 4 C n 1 5 C n 1 6 C n 1 7 G n 1 8 A n 1 9 A n 1 10 A n 1 11 G n 1 12 G n 1 13 A n 1 14 U n 1 15 G n 1 16 G n 1 17 C n 1 18 G n 1 19 G n 1 20 A n 1 21 A n 1 22 A n 1 23 C n 1 24 G n 1 25 C n 1 26 C n 1 27 A n 1 28 G n 1 29 A n 1 30 U n 1 31 G n 1 32 C n 1 33 C n 1 34 U n 1 35 U n 1 36 G n 1 37 U n 1 38 A n 1 39 A n 1 40 C n 1 41 C n 1 42 G n 1 43 A n 1 44 A n 1 45 A n 1 46 G n 1 47 G n 1 48 G n 1 49 G n 1 50 G n 1 51 A n 1 52 A n 1 53 U 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'RNA was prepared by In vitro transcription' # 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 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HOH non-polymer . WATER ? 'H2 O' 18.015 SAM non-polymer . S-ADENOSYLMETHIONINE ? 'C15 H22 N6 O5 S' 398.437 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 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 GTP 1 1 1 GTP GTP A . n A 1 2 U 2 2 2 U URI A . n A 1 3 U 3 3 3 U URI A . n A 1 4 C 4 4 4 C CYT A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 C 6 6 6 C CYT A . n A 1 7 G 7 7 7 G GUA A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 A 9 9 9 A ADE A . n A 1 10 A 10 10 10 A ADE A . n A 1 11 G 11 11 11 G GUA A . n A 1 12 G 12 12 12 G GUA A . n A 1 13 A 13 13 13 A ADE A . n A 1 14 U 14 14 14 U URI A . n A 1 15 G 15 15 15 G GUA A . n A 1 16 G 16 16 16 G GUA A . n A 1 17 C 17 17 17 C CYT A . n A 1 18 G 18 18 18 G GUA A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 A 20 20 20 A ADE A . n A 1 21 A 21 21 21 A ADE A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 C 23 23 23 C CYT A . n A 1 24 G 24 24 24 G GUA A . n A 1 25 C 25 25 25 C CYT A . n A 1 26 C 26 26 26 C CYT A . n A 1 27 A 27 27 27 A ADE A . n A 1 28 G 28 28 28 G GUA A . n A 1 29 A 29 29 29 A ADE A . n A 1 30 U 30 30 30 U URI A . n A 1 31 G 31 31 31 G GUA A . n A 1 32 C 32 32 32 C CYT A . n A 1 33 C 33 33 33 C CYT A . n A 1 34 U 34 34 34 U URI A . n A 1 35 U 35 35 35 U URI A . n A 1 36 G 36 36 36 G GUA A . n A 1 37 U 37 37 37 U URI A . n A 1 38 A 38 38 38 A ADE A . n A 1 39 A 39 39 39 A ADE A . n A 1 40 C 40 40 40 C CYT A . n A 1 41 C 41 41 41 C CYT A . n A 1 42 G 42 42 42 G GUA A . n A 1 43 A 43 43 43 A ADE A . n A 1 44 A 44 44 44 A ADE A . n A 1 45 A 45 45 45 A ADE A . n A 1 46 G 46 46 46 G GUA A . n A 1 47 G 47 47 47 G GUA A . n A 1 48 G 48 48 48 G GUA A . n A 1 49 G 49 49 49 G GUA A . n A 1 50 G 50 50 50 G GUA A . n A 1 51 A 51 51 51 A ADE A . n A 1 52 A 52 52 52 A ADE A . n A 1 53 U 53 53 53 U URI A . 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 B 2 SR 1 201 201 SR SR A . C 2 SR 1 202 202 SR SR A . D 2 SR 1 203 203 SR SR A . E 2 SR 1 204 204 SR SR A . F 2 SR 1 205 205 SR SR A . G 2 SR 1 206 206 SR SR A . H 2 SR 1 207 207 SR SR A . I 2 SR 1 208 208 SR SR A . J 2 SR 1 209 209 SR SR A . K 2 SR 1 210 210 SR SR A . L 2 SR 1 211 211 SR SR A . M 2 SR 1 212 212 SR SR A . N 2 SR 1 213 213 SR SR A . O 2 SR 1 214 214 SR SR A . P 2 SR 1 215 215 SR SR A . Q 3 SAM 1 216 1 SAM SAM A . R 4 HOH 1 217 1 HOH HOH A . R 4 HOH 2 218 2 HOH HOH A . R 4 HOH 3 219 3 HOH HOH A . R 4 HOH 4 220 4 HOH HOH A . R 4 HOH 5 221 5 HOH HOH A . R 4 HOH 6 222 6 HOH HOH A . R 4 HOH 7 223 7 HOH HOH A . R 4 HOH 8 224 8 HOH HOH A . R 4 HOH 9 225 9 HOH HOH A . R 4 HOH 10 226 10 HOH HOH A . R 4 HOH 11 227 11 HOH HOH A . R 4 HOH 12 228 12 HOH HOH A . R 4 HOH 13 229 13 HOH HOH A . R 4 HOH 14 230 14 HOH HOH A . R 4 HOH 15 231 15 HOH HOH A . R 4 HOH 16 232 16 HOH HOH A . R 4 HOH 17 233 17 HOH HOH A . R 4 HOH 18 234 18 HOH HOH A . R 4 HOH 19 235 19 HOH HOH A . R 4 HOH 20 236 20 HOH HOH A . R 4 HOH 21 237 21 HOH HOH A . R 4 HOH 22 238 22 HOH HOH A . R 4 HOH 23 239 23 HOH HOH A . R 4 HOH 24 240 24 HOH HOH A . R 4 HOH 25 241 25 HOH HOH A . R 4 HOH 26 242 26 HOH HOH A . R 4 HOH 27 243 27 HOH HOH A . R 4 HOH 28 244 28 HOH HOH A . R 4 HOH 29 245 29 HOH HOH A . R 4 HOH 30 246 30 HOH HOH A . R 4 HOH 31 247 31 HOH HOH A . R 4 HOH 32 248 32 HOH HOH A . R 4 HOH 33 249 33 HOH HOH A . R 4 HOH 34 250 34 HOH HOH A . R 4 HOH 35 251 35 HOH HOH A . R 4 HOH 36 252 36 HOH HOH A . R 4 HOH 37 253 37 HOH HOH A . R 4 HOH 38 254 38 HOH HOH A . R 4 HOH 39 255 39 HOH HOH A . R 4 HOH 40 256 40 HOH HOH A . R 4 HOH 41 257 41 HOH HOH A . R 4 HOH 42 258 42 HOH HOH A . R 4 HOH 43 259 43 HOH HOH A . R 4 HOH 44 260 44 HOH HOH A . R 4 HOH 45 261 45 HOH HOH A . R 4 HOH 46 262 46 HOH HOH A . R 4 HOH 47 263 47 HOH HOH A . R 4 HOH 48 264 48 HOH HOH A . R 4 HOH 49 265 49 HOH HOH A . R 4 HOH 50 266 50 HOH HOH A . R 4 HOH 51 267 51 HOH HOH A . R 4 HOH 52 268 52 HOH HOH A . R 4 HOH 53 269 53 HOH HOH A . R 4 HOH 54 270 54 HOH HOH A . R 4 HOH 55 271 55 HOH HOH A . R 4 HOH 56 272 56 HOH HOH A . R 4 HOH 57 273 57 HOH HOH A . R 4 HOH 58 274 58 HOH HOH A . R 4 HOH 59 275 59 HOH HOH A . R 4 HOH 60 276 60 HOH HOH A . R 4 HOH 61 277 61 HOH HOH A . R 4 HOH 62 278 62 HOH HOH A . R 4 HOH 63 279 63 HOH HOH A . R 4 HOH 64 280 64 HOH HOH A . R 4 HOH 65 281 65 HOH HOH A . R 4 HOH 66 282 66 HOH HOH A . R 4 HOH 67 283 67 HOH HOH A . R 4 HOH 68 284 68 HOH HOH A . R 4 HOH 69 285 69 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.2 ? 1 HKL-2000 'data collection' . ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 PHASER phasing . ? 5 # _cell.entry_id 3E5C _cell.length_a 97.806 _cell.length_b 97.806 _cell.length_c 87.138 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3E5C _symmetry.space_group_name_H-M 'I 41 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3E5C _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.99 _exptl_crystal.density_percent_sol 58.91 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details '40 mM sodium cacodylate, 80 mM SrCl, 15% MPD, 2 mM spermine-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'sodium cacodylate' ? ? ? 1 2 1 SrCl ? ? ? 1 3 1 MPD ? ? ? 1 4 1 spermine-HCl ? ? ? 1 5 2 'sodium cacodylate' ? ? ? 1 6 2 SrCl ? ? ? 1 7 2 MPD ? ? ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315' 2007-11-21 ? 2 CCD 'ADSC QUANTUM 210' 2007-10-22 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M ? 'SINGLE WAVELENGTH' x-ray 2 1 M ? 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9792 1.0 2 0.918 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'APS BEAMLINE 24-ID-E' APS 24-ID-E ? 0.9792 2 SYNCHROTRON 'CHESS BEAMLINE F1' CHESS F1 ? 0.918 # _reflns.entry_id 3E5C _reflns.observed_criterion_sigma_I 37.1 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20 _reflns.d_resolution_high 2.25 _reflns.number_obs 9607 _reflns.number_all ? _reflns.percent_possible_obs 93.3 _reflns.pdbx_Rmerge_I_obs 0.069 _reflns.pdbx_Rsym_value 0.065 _reflns.pdbx_netI_over_sigmaI 24.7 _reflns.B_iso_Wilson_estimate 47.8 _reflns.pdbx_redundancy 9.8 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.25 _reflns_shell.d_res_low 2.35 _reflns_shell.percent_possible_all 74 _reflns_shell.Rmerge_I_obs .37 _reflns_shell.pdbx_Rsym_value .417 _reflns_shell.meanI_over_sigI_obs 1.6 _reflns_shell.pdbx_redundancy 4.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 666 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3E5C _refine.ls_number_reflns_obs 9607 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 1443315.13 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 19.90 _refine.ls_d_res_high 2.25 _refine.ls_percent_reflns_obs 93.3 _refine.ls_R_factor_obs 0.221 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.221 _refine.ls_R_factor_R_free 0.227 _refine.ls_R_factor_R_free_error 0.011 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 460 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 54.5 _refine.aniso_B[1][1] -8.63 _refine.aniso_B[2][2] -8.63 _refine.aniso_B[3][3] 17.26 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.4 _refine.solvent_model_param_bsol 56.7208 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'BULK SOLVENT MODEL USED' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD+MR _refine.pdbx_isotropic_thermal_model RESTRAINED _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.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 3E5C _refine_analyze.Luzzati_coordinate_error_obs 0.30 _refine_analyze.Luzzati_sigma_a_obs 0.40 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.35 _refine_analyze.Luzzati_sigma_a_free 0.43 _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_Luzzati_d_res_high_obs ? _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 1155 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 69 _refine_hist.number_atoms_total 1266 _refine_hist.d_res_high 2.25 _refine_hist.d_res_low 19.90 # 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 c_bond_d 0.011 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.7 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 19.2 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.54 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.25 _refine_ls_shell.d_res_low 2.39 _refine_ls_shell.number_reflns_R_work 1108 _refine_ls_shell.R_factor_R_work 0.341 _refine_ls_shell.percent_reflns_obs 69.4 _refine_ls_shell.R_factor_R_free 0.335 _refine_ls_shell.R_factor_R_free_error 0.043 _refine_ls_shell.percent_reflns_R_free 5.3 _refine_ls_shell.number_reflns_R_free 62 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 ion.param ion.top 'X-RAY DIFFRACTION' 2 water_rep.param dna-rna.top 'X-RAY DIFFRACTION' 3 dna-rna_rep.param water.top 'X-RAY DIFFRACTION' 4 gtp.param gtp.top 'X-RAY DIFFRACTION' 5 samtest.param samtest.top 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3E5C _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 3E5C _struct.title 'Crystal Structure of the SMK box (SAM-III) Riboswitch with SAM' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3E5C _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'SAM riboswitch SMK SAM-III translation regulation SD, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 2 ? Q N N 3 ? R N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3E5C _struct_ref.pdbx_db_accession 3E5C _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code GUUCCCGAAAGGAUGGCGGAAACGCCAGAUGCCUUGUAACCGAAAGGGGGAAU _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3E5C _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 53 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3E5C _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 53 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 53 # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A GTP 1 "O3'" ? ? ? 1_555 A U 2 P ? ? A GTP 1 A U 2 1_555 ? ? ? ? ? ? ? 1.700 ? ? metalc1 metalc ? ? A GTP 1 O2A ? ? ? 1_555 M SR . SR ? ? A GTP 1 A SR 212 1_555 ? ? ? ? ? ? ? 2.648 ? ? metalc2 metalc ? ? A C 6 OP2 ? ? ? 1_555 H SR . SR ? ? A C 6 A SR 207 1_555 ? ? ? ? ? ? ? 2.556 ? ? metalc3 metalc ? ? A U 14 O4 ? ? ? 1_555 N SR . SR ? ? A U 14 A SR 213 1_555 ? ? ? ? ? ? ? 2.533 ? ? metalc4 metalc ? ? A A 38 OP2 ? ? ? 1_555 P SR . SR ? ? A A 38 A SR 215 1_555 ? ? ? ? ? ? ? 2.411 ? ? metalc5 metalc ? ? H SR . SR ? ? ? 1_555 R HOH . O ? ? A SR 207 A HOH 282 1_555 ? ? ? ? ? ? ? 2.554 ? ? metalc6 metalc ? ? I SR . SR ? ? ? 1_555 R HOH . O ? ? A SR 208 A HOH 224 1_555 ? ? ? ? ? ? ? 2.411 ? ? hydrog1 hydrog ? ? A GTP 1 N1 ? ? ? 1_555 A U 53 O2 ? ? A GTP 1 A U 53 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog2 hydrog ? ? A GTP 1 O6 ? ? ? 1_555 A U 53 N3 ? ? A GTP 1 A U 53 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A U 2 N3 ? ? ? 1_555 A A 52 N1 ? ? A U 2 A A 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 O4 ? ? ? 1_555 A A 52 N6 ? ? A U 2 A A 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 51 N1 ? ? A U 3 A A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 51 N6 ? ? A U 3 A A 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 4 N3 ? ? ? 1_555 A G 50 N1 ? ? A C 4 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 4 N4 ? ? ? 1_555 A G 50 O6 ? ? A C 4 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 O2 ? ? ? 1_555 A G 50 N2 ? ? A C 4 A G 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 49 N1 ? ? A C 5 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 49 O6 ? ? A C 5 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 49 N2 ? ? A C 5 A G 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 48 N1 ? ? A C 6 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 48 O6 ? ? A C 6 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 48 N2 ? ? A C 6 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N6 ? ? ? 1_555 A G 36 N3 ? ? A A 8 A G 36 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog17 hydrog ? ? A A 8 N7 ? ? ? 1_555 A G 36 N2 ? ? A A 8 A G 36 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog18 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 35 N3 ? ? A A 9 A U 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 35 O4 ? ? A A 9 A U 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 34 N3 ? ? A A 10 A U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 34 O4 ? ? A A 10 A U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 33 N3 ? ? A G 11 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 33 O2 ? ? A G 11 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 33 N4 ? ? A G 11 A C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 32 N3 ? ? A G 12 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 32 O2 ? ? A G 12 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 32 N4 ? ? A G 12 A C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 13 N1 ? ? ? 1_555 A G 28 N1 ? ? A A 13 A G 28 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog29 hydrog ? ? A A 13 N6 ? ? ? 1_555 A G 28 O6 ? ? A A 13 A G 28 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog30 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 27 N1 ? ? A U 14 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 27 N6 ? ? A U 14 A A 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 15 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 15 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 15 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 15 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 15 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 15 A C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 16 N1 ? ? ? 1_555 A C 25 N3 ? ? A G 16 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 16 N2 ? ? ? 1_555 A C 25 O2 ? ? A G 16 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 16 O6 ? ? ? 1_555 A C 25 N4 ? ? A G 16 A C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 17 N3 ? ? ? 1_555 A G 24 N1 ? ? A C 17 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 17 N4 ? ? ? 1_555 A G 24 O6 ? ? A C 17 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 17 O2 ? ? ? 1_555 A G 24 N2 ? ? A C 17 A G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 18 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 18 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 18 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 18 A C 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 19 N2 ? ? ? 1_555 A A 22 N7 ? ? A G 19 A A 22 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog45 hydrog ? ? A G 31 N7 ? ? ? 1_555 A G 36 N1 ? ? A G 31 A G 36 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog46 hydrog ? ? A G 31 O6 ? ? ? 1_555 A G 36 N2 ? ? A G 31 A G 36 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog47 hydrog ? ? A A 38 N1 ? ? ? 1_555 A G 48 N2 ? ? A A 38 A G 48 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog48 hydrog ? ? A A 38 N6 ? ? ? 1_555 A G 48 N3 ? ? A A 38 A G 48 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog49 hydrog ? ? A C 40 N3 ? ? ? 1_555 A G 47 N1 ? ? A C 40 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 40 N4 ? ? ? 1_555 A G 47 O6 ? ? A C 40 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 40 O2 ? ? ? 1_555 A G 47 N2 ? ? A C 40 A G 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 41 N3 ? ? ? 1_555 A G 46 N1 ? ? A C 41 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 41 N4 ? ? ? 1_555 A G 46 O6 ? ? A C 41 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 41 O2 ? ? ? 1_555 A G 46 N2 ? ? A C 41 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 42 N2 ? ? ? 1_555 A A 45 N7 ? ? A G 42 A A 45 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _pdbx_struct_conn_angle.id 1 _pdbx_struct_conn_angle.ptnr1_label_atom_id OP2 _pdbx_struct_conn_angle.ptnr1_label_alt_id ? _pdbx_struct_conn_angle.ptnr1_label_asym_id A _pdbx_struct_conn_angle.ptnr1_label_comp_id C _pdbx_struct_conn_angle.ptnr1_label_seq_id 6 _pdbx_struct_conn_angle.ptnr1_auth_atom_id ? _pdbx_struct_conn_angle.ptnr1_auth_asym_id A _pdbx_struct_conn_angle.ptnr1_auth_comp_id C _pdbx_struct_conn_angle.ptnr1_auth_seq_id 6 _pdbx_struct_conn_angle.ptnr1_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr1_symmetry 1_555 _pdbx_struct_conn_angle.ptnr2_label_atom_id SR _pdbx_struct_conn_angle.ptnr2_label_alt_id ? _pdbx_struct_conn_angle.ptnr2_label_asym_id H _pdbx_struct_conn_angle.ptnr2_label_comp_id SR _pdbx_struct_conn_angle.ptnr2_label_seq_id . _pdbx_struct_conn_angle.ptnr2_auth_atom_id ? _pdbx_struct_conn_angle.ptnr2_auth_asym_id A _pdbx_struct_conn_angle.ptnr2_auth_comp_id SR _pdbx_struct_conn_angle.ptnr2_auth_seq_id 207 _pdbx_struct_conn_angle.ptnr2_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr2_symmetry 1_555 _pdbx_struct_conn_angle.ptnr3_label_atom_id O _pdbx_struct_conn_angle.ptnr3_label_alt_id ? _pdbx_struct_conn_angle.ptnr3_label_asym_id R _pdbx_struct_conn_angle.ptnr3_label_comp_id HOH _pdbx_struct_conn_angle.ptnr3_label_seq_id . _pdbx_struct_conn_angle.ptnr3_auth_atom_id ? _pdbx_struct_conn_angle.ptnr3_auth_asym_id A _pdbx_struct_conn_angle.ptnr3_auth_comp_id HOH _pdbx_struct_conn_angle.ptnr3_auth_seq_id 282 _pdbx_struct_conn_angle.ptnr3_PDB_ins_code ? _pdbx_struct_conn_angle.ptnr3_symmetry 1_555 _pdbx_struct_conn_angle.value 150.6 _pdbx_struct_conn_angle.value_esd ? # 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 SR 204 ? 1 'BINDING SITE FOR RESIDUE SR A 204' AC3 Software A SR 207 ? 2 'BINDING SITE FOR RESIDUE SR A 207' AC4 Software A SR 208 ? 1 'BINDING SITE FOR RESIDUE SR A 208' AC7 Software A SAM 216 ? 2 'BINDING SITE FOR RESIDUE SAM A 216' # 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 1 HOH R . ? HOH A 223 . ? 1_555 ? 2 AC3 2 HOH R . ? HOH A 219 . ? 1_555 ? 3 AC3 2 HOH R . ? HOH A 282 . ? 1_555 ? 4 AC4 1 HOH R . ? HOH A 224 . ? 1_555 ? 5 AC7 2 HOH R . ? HOH A 239 . ? 1_555 ? 6 AC7 2 HOH R . ? HOH A 273 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O1B A GTP 1 ? ? O A HOH 284 ? ? 1.98 2 1 O2A A GTP 1 ? ? O A HOH 275 ? ? 2.17 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 GTP _pdbx_validate_rmsd_bond.auth_seq_id_1 1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 P _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 U _pdbx_validate_rmsd_bond.auth_seq_id_2 2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.700 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation 0.093 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # 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 C 4 ? ? "C1'" A C 4 ? ? N1 A C 4 ? ? 112.99 108.50 4.49 0.70 N 2 1 "C3'" A G 28 ? ? "O3'" A G 28 ? ? P A A 29 ? ? 128.49 119.70 8.79 1.20 Y 3 1 "O4'" A G 36 ? ? "C1'" A G 36 ? ? N9 A G 36 ? ? 114.90 108.50 6.40 0.70 N 4 1 "O4'" A G 48 ? ? "C1'" A G 48 ? ? N9 A G 48 ? ? 112.89 108.50 4.39 0.70 N # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id GTP _pdbx_struct_mod_residue.label_seq_id 1 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id GTP _pdbx_struct_mod_residue.auth_seq_id 1 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id G _pdbx_struct_mod_residue.details "GUANOSINE-5'-TRIPHOSPHATE" # 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 GTP PG P N N 111 GTP O1G O N N 112 GTP O2G O N N 113 GTP O3G O N N 114 GTP O3B O N N 115 GTP PB P N N 116 GTP O1B O N N 117 GTP O2B O N N 118 GTP O3A O N N 119 GTP PA P N N 120 GTP O1A O N N 121 GTP O2A O N N 122 GTP "O5'" O N N 123 GTP "C5'" C N N 124 GTP "C4'" C N R 125 GTP "O4'" O N N 126 GTP "C3'" C N S 127 GTP "O3'" O N N 128 GTP "C2'" C N R 129 GTP "O2'" O N N 130 GTP "C1'" C N R 131 GTP N9 N Y N 132 GTP C8 C Y N 133 GTP N7 N Y N 134 GTP C5 C Y N 135 GTP C6 C N N 136 GTP O6 O N N 137 GTP N1 N N N 138 GTP C2 C N N 139 GTP N2 N N N 140 GTP N3 N N N 141 GTP C4 C Y N 142 GTP HOG2 H N N 143 GTP HOG3 H N N 144 GTP HOB2 H N N 145 GTP HOA2 H N N 146 GTP "H5'" H N N 147 GTP "H5''" H N N 148 GTP "H4'" H N N 149 GTP "H3'" H N N 150 GTP "HO3'" H N N 151 GTP "H2'" H N N 152 GTP "HO2'" H N N 153 GTP "H1'" H N N 154 GTP H8 H N N 155 GTP HN1 H N N 156 GTP HN21 H N N 157 GTP HN22 H N N 158 HOH O O N N 159 HOH H1 H N N 160 HOH H2 H N N 161 SAM N N N N 162 SAM CA C N S 163 SAM C C N N 164 SAM O O N N 165 SAM OXT O N N 166 SAM CB C N N 167 SAM CG C N N 168 SAM SD S N S 169 SAM CE C N N 170 SAM "C5'" C N N 171 SAM "C4'" C N S 172 SAM "O4'" O N N 173 SAM "C3'" C N S 174 SAM "O3'" O N N 175 SAM "C2'" C N R 176 SAM "O2'" O N N 177 SAM "C1'" C N R 178 SAM N9 N Y N 179 SAM C8 C Y N 180 SAM N7 N Y N 181 SAM C5 C Y N 182 SAM C6 C Y N 183 SAM N6 N N N 184 SAM N1 N Y N 185 SAM C2 C Y N 186 SAM N3 N Y N 187 SAM C4 C Y N 188 SAM HN1 H N N 189 SAM HN2 H N N 190 SAM HA H N N 191 SAM HB1 H N N 192 SAM HB2 H N N 193 SAM HG1 H N N 194 SAM HG2 H N N 195 SAM HE1 H N N 196 SAM HE2 H N N 197 SAM HE3 H N N 198 SAM "H5'1" H N N 199 SAM "H5'2" H N N 200 SAM "H4'" H N N 201 SAM "H3'" H N N 202 SAM "HO3'" H N N 203 SAM "H2'" H N N 204 SAM "HO2'" H N N 205 SAM "H1'" H N N 206 SAM H8 H N N 207 SAM HN61 H N N 208 SAM HN62 H N N 209 SAM H2 H N N 210 SR SR SR N N 211 U OP3 O N N 212 U P P N N 213 U OP1 O N N 214 U OP2 O N N 215 U "O5'" O N N 216 U "C5'" C N N 217 U "C4'" C N R 218 U "O4'" O N N 219 U "C3'" C N S 220 U "O3'" O N N 221 U "C2'" C N R 222 U "O2'" O N N 223 U "C1'" C N R 224 U N1 N N N 225 U C2 C N N 226 U O2 O N N 227 U N3 N N N 228 U C4 C N N 229 U O4 O N N 230 U C5 C N N 231 U C6 C N N 232 U HOP3 H N N 233 U HOP2 H N N 234 U "H5'" H N N 235 U "H5''" H N N 236 U "H4'" H N N 237 U "H3'" H N N 238 U "HO3'" H N N 239 U "H2'" H N N 240 U "HO2'" H N N 241 U "H1'" H N N 242 U H3 H N N 243 U H5 H N N 244 U H6 H N N 245 # 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 GTP PG O1G doub N N 116 GTP PG O2G sing N N 117 GTP PG O3G sing N N 118 GTP PG O3B sing N N 119 GTP O2G HOG2 sing N N 120 GTP O3G HOG3 sing N N 121 GTP O3B PB sing N N 122 GTP PB O1B doub N N 123 GTP PB O2B sing N N 124 GTP PB O3A sing N N 125 GTP O2B HOB2 sing N N 126 GTP O3A PA sing N N 127 GTP PA O1A doub N N 128 GTP PA O2A sing N N 129 GTP PA "O5'" sing N N 130 GTP O2A HOA2 sing N N 131 GTP "O5'" "C5'" sing N N 132 GTP "C5'" "C4'" sing N N 133 GTP "C5'" "H5'" sing N N 134 GTP "C5'" "H5''" sing N N 135 GTP "C4'" "O4'" sing N N 136 GTP "C4'" "C3'" sing N N 137 GTP "C4'" "H4'" sing N N 138 GTP "O4'" "C1'" sing N N 139 GTP "C3'" "O3'" sing N N 140 GTP "C3'" "C2'" sing N N 141 GTP "C3'" "H3'" sing N N 142 GTP "O3'" "HO3'" sing N N 143 GTP "C2'" "O2'" sing N N 144 GTP "C2'" "C1'" sing N N 145 GTP "C2'" "H2'" sing N N 146 GTP "O2'" "HO2'" sing N N 147 GTP "C1'" N9 sing N N 148 GTP "C1'" "H1'" sing N N 149 GTP N9 C8 sing Y N 150 GTP N9 C4 sing Y N 151 GTP C8 N7 doub Y N 152 GTP C8 H8 sing N N 153 GTP N7 C5 sing Y N 154 GTP C5 C6 sing N N 155 GTP C5 C4 doub Y N 156 GTP C6 O6 doub N N 157 GTP C6 N1 sing N N 158 GTP N1 C2 sing N N 159 GTP N1 HN1 sing N N 160 GTP C2 N2 sing N N 161 GTP C2 N3 doub N N 162 GTP N2 HN21 sing N N 163 GTP N2 HN22 sing N N 164 GTP N3 C4 sing N N 165 HOH O H1 sing N N 166 HOH O H2 sing N N 167 SAM N CA sing N N 168 SAM N HN1 sing N N 169 SAM N HN2 sing N N 170 SAM CA C sing N N 171 SAM CA CB sing N N 172 SAM CA HA sing N N 173 SAM C O doub N N 174 SAM C OXT sing N N 175 SAM CB CG sing N N 176 SAM CB HB1 sing N N 177 SAM CB HB2 sing N N 178 SAM CG SD sing N N 179 SAM CG HG1 sing N N 180 SAM CG HG2 sing N N 181 SAM SD CE sing N N 182 SAM SD "C5'" sing N N 183 SAM CE HE1 sing N N 184 SAM CE HE2 sing N N 185 SAM CE HE3 sing N N 186 SAM "C5'" "C4'" sing N N 187 SAM "C5'" "H5'1" sing N N 188 SAM "C5'" "H5'2" sing N N 189 SAM "C4'" "O4'" sing N N 190 SAM "C4'" "C3'" sing N N 191 SAM "C4'" "H4'" sing N N 192 SAM "O4'" "C1'" sing N N 193 SAM "C3'" "O3'" sing N N 194 SAM "C3'" "C2'" sing N N 195 SAM "C3'" "H3'" sing N N 196 SAM "O3'" "HO3'" sing N N 197 SAM "C2'" "O2'" sing N N 198 SAM "C2'" "C1'" sing N N 199 SAM "C2'" "H2'" sing N N 200 SAM "O2'" "HO2'" sing N N 201 SAM "C1'" N9 sing N N 202 SAM "C1'" "H1'" sing N N 203 SAM N9 C8 sing Y N 204 SAM N9 C4 sing Y N 205 SAM C8 N7 doub Y N 206 SAM C8 H8 sing N N 207 SAM N7 C5 sing Y N 208 SAM C5 C6 sing Y N 209 SAM C5 C4 doub Y N 210 SAM C6 N6 sing N N 211 SAM C6 N1 doub Y N 212 SAM N6 HN61 sing N N 213 SAM N6 HN62 sing N N 214 SAM N1 C2 sing Y N 215 SAM C2 N3 doub Y N 216 SAM C2 H2 sing N N 217 SAM N3 C4 sing Y N 218 U OP3 P sing N N 219 U OP3 HOP3 sing N N 220 U P OP1 doub N N 221 U P OP2 sing N N 222 U P "O5'" sing N N 223 U OP2 HOP2 sing N N 224 U "O5'" "C5'" sing N N 225 U "C5'" "C4'" sing N N 226 U "C5'" "H5'" sing N N 227 U "C5'" "H5''" sing N N 228 U "C4'" "O4'" sing N N 229 U "C4'" "C3'" sing N N 230 U "C4'" "H4'" sing N N 231 U "O4'" "C1'" sing N N 232 U "C3'" "O3'" sing N N 233 U "C3'" "C2'" sing N N 234 U "C3'" "H3'" sing N N 235 U "O3'" "HO3'" sing N N 236 U "C2'" "O2'" sing N N 237 U "C2'" "C1'" sing N N 238 U "C2'" "H2'" sing N N 239 U "O2'" "HO2'" sing N N 240 U "C1'" N1 sing N N 241 U "C1'" "H1'" sing N N 242 U N1 C2 sing N N 243 U N1 C6 sing N N 244 U C2 O2 doub N N 245 U C2 N3 sing N N 246 U N3 C4 sing N N 247 U N3 H3 sing N N 248 U C4 O4 doub N N 249 U C4 C5 sing N N 250 U C5 C6 doub N N 251 U C5 H5 sing N N 252 U C6 H6 sing N N 253 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3E5C 'double helix' 3E5C 'a-form double helix' 3E5C tetraloop 3E5C 'bulge loop' 3E5C 'mismatched base pair' 3E5C 'three-way junction' # 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 GTP 1 1_555 A U 53 1_555 -2.353 -0.713 0.083 1.838 -9.695 -2.869 1 A_GTP1:U53_A A 1 ? A 53 ? 28 ? 1 A U 2 1_555 A A 52 1_555 -0.127 -0.190 0.111 5.611 -17.950 3.481 2 A_U2:A52_A A 2 ? A 52 ? 20 1 1 A U 3 1_555 A A 51 1_555 -0.077 -0.179 -0.005 9.538 -15.145 5.810 3 A_U3:A51_A A 3 ? A 51 ? 20 1 1 A C 4 1_555 A G 50 1_555 0.183 -0.115 -0.124 8.479 -13.917 1.787 4 A_C4:G50_A A 4 ? A 50 ? 19 1 1 A C 5 1_555 A G 49 1_555 0.435 -0.040 -0.290 10.488 -5.278 1.974 5 A_C5:G49_A A 5 ? A 49 ? 19 1 1 A C 6 1_555 A G 48 1_555 0.537 -0.242 -0.512 15.149 -7.510 2.002 6 A_C6:G48_A A 6 ? A 48 ? 19 1 1 A A 22 1_555 A G 19 1_555 -6.811 -4.737 0.593 -14.278 3.273 -16.249 7 A_A22:G19_A A 22 ? A 19 ? ? ? 1 A C 23 1_555 A G 18 1_555 0.107 -0.077 0.075 -1.068 0.693 1.340 8 A_C23:G18_A A 23 ? A 18 ? 19 1 1 A G 24 1_555 A C 17 1_555 -0.421 -0.284 0.295 7.481 -10.604 -1.935 9 A_G24:C17_A A 24 ? A 17 ? 19 1 1 A C 25 1_555 A G 16 1_555 1.105 -0.297 -0.079 7.533 -14.586 9.640 10 A_C25:G16_A A 25 ? A 16 ? 19 1 1 A C 26 1_555 A G 15 1_555 1.112 -0.405 0.394 -4.393 -16.131 8.692 11 A_C26:G15_A A 26 ? A 15 ? 19 1 1 A A 27 1_555 A U 14 1_555 -0.913 -0.126 0.485 -7.361 -13.969 2.405 12 A_A27:U14_A A 27 ? A 14 ? 20 1 1 A G 28 1_555 A A 13 1_555 0.362 1.549 0.390 10.248 -18.496 -15.382 13 A_G28:A13_A A 28 ? A 13 ? 8 1 1 A C 32 1_555 A G 12 1_555 0.107 -0.042 -0.050 3.208 -8.196 4.912 14 A_C32:G12_A A 32 ? A 12 ? 19 1 1 A C 33 1_555 A G 11 1_555 0.191 -0.098 -0.131 -0.970 -7.272 1.335 15 A_C33:G11_A A 33 ? A 11 ? 19 1 1 A U 34 1_555 A A 10 1_555 0.136 -0.157 -0.170 2.064 -2.233 -0.510 16 A_U34:A10_A A 34 ? A 10 ? 20 1 1 A U 35 1_555 A A 9 1_555 -0.041 -0.016 -0.225 14.798 0.001 10.762 17 A_U35:A9_A A 35 ? A 9 ? 20 1 1 A G 36 1_555 A G 31 1_555 5.039 0.058 0.272 21.407 11.380 -114.940 18 A_G36:G31_A A 36 ? A 31 ? 7 ? 1 A C 40 1_555 A G 47 1_555 0.378 -0.260 -0.180 1.691 -11.541 2.601 19 A_C40:G47_A A 40 ? A 47 ? 19 1 1 A C 41 1_555 A G 46 1_555 0.416 -0.288 -0.057 -0.966 0.320 -1.874 20 A_C41:G46_A A 41 ? A 46 ? 19 1 1 A G 42 1_555 A A 45 1_555 7.962 -5.093 0.861 9.365 -7.948 -46.770 21 A_G42:A45_A A 42 ? A 45 ? ? ? # 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 GTP 1 1_555 A U 53 1_555 A U 2 1_555 A A 52 1_555 0.067 -0.916 3.140 -3.131 7.916 42.406 -1.969 -0.378 2.920 10.813 4.277 43.213 1 AA_GTP1U2:A52U53_AA A 1 ? A 53 ? A 2 ? A 52 ? 1 A U 2 1_555 A A 52 1_555 A U 3 1_555 A A 51 1_555 0.007 -0.949 3.106 -2.163 7.148 33.297 -2.664 -0.328 2.841 12.283 3.716 34.101 2 AA_U2U3:A51A52_AA A 2 ? A 52 ? A 3 ? A 51 ? 1 A U 3 1_555 A A 51 1_555 A C 4 1_555 A G 50 1_555 -0.103 -1.546 3.283 -1.525 2.677 34.209 -3.032 -0.061 3.158 4.539 2.587 34.344 3 AA_U3C4:G50A51_AA A 3 ? A 51 ? A 4 ? A 50 ? 1 A C 4 1_555 A G 50 1_555 A C 5 1_555 A G 49 1_555 -0.727 -1.919 3.243 -2.043 7.135 29.084 -5.075 1.013 2.748 13.924 3.986 29.996 4 AA_C4C5:G49G50_AA A 4 ? A 50 ? A 5 ? A 49 ? 1 A C 5 1_555 A G 49 1_555 A C 6 1_555 A G 48 1_555 -0.398 -1.706 3.275 -1.703 6.085 27.351 -4.880 0.440 2.855 12.656 3.541 28.058 5 AA_C5C6:G48G49_AA A 5 ? A 49 ? A 6 ? A 48 ? 1 A A 22 1_555 A G 19 1_555 A C 23 1_555 A G 18 1_555 2.059 -1.076 2.908 3.684 5.679 49.799 -1.632 -2.189 2.912 6.708 -4.351 50.228 6 AA_A22C23:G18G19_AA A 22 ? A 19 ? A 23 ? A 18 ? 1 A C 23 1_555 A G 18 1_555 A G 24 1_555 A C 17 1_555 -0.805 -1.977 2.935 -2.347 2.575 24.892 -5.210 1.242 2.782 5.936 5.412 25.131 7 AA_C23G24:C17G18_AA A 23 ? A 18 ? A 24 ? A 17 ? 1 A G 24 1_555 A C 17 1_555 A C 25 1_555 A G 16 1_555 0.928 -1.514 3.239 2.717 2.949 36.961 -2.761 -1.100 3.171 4.635 -4.271 37.170 8 AA_G24C25:G16C17_AA A 24 ? A 17 ? A 25 ? A 16 ? 1 A C 25 1_555 A G 16 1_555 A C 26 1_555 A G 15 1_555 -0.030 -1.864 3.355 -0.199 13.180 32.898 -4.860 0.022 2.452 22.195 0.334 35.372 9 AA_C25C26:G15G16_AA A 25 ? A 16 ? A 26 ? A 15 ? 1 A C 26 1_555 A G 15 1_555 A A 27 1_555 A U 14 1_555 -0.710 -1.876 2.662 -1.169 19.457 25.695 -5.597 1.149 1.047 37.617 2.260 32.152 10 AA_C26A27:U14G15_AA A 26 ? A 15 ? A 27 ? A 14 ? 1 A A 27 1_555 A U 14 1_555 A G 28 1_555 A A 13 1_555 -1.317 -0.723 3.009 1.964 3.803 32.792 -1.846 2.611 2.828 6.700 -3.460 33.063 11 AA_A27G28:A13U14_AA A 27 ? A 14 ? A 28 ? A 13 ? 1 A G 28 1_555 A A 13 1_555 A C 32 1_555 A G 12 1_555 -1.257 -2.384 2.895 -2.770 13.720 50.499 -3.437 1.279 2.281 15.738 3.177 52.280 12 AA_G28C32:G12A13_AA A 28 ? A 13 ? A 32 ? A 12 ? 1 A C 32 1_555 A G 12 1_555 A C 33 1_555 A G 11 1_555 -1.037 -2.212 3.196 -1.744 8.763 30.445 -5.493 1.611 2.531 16.252 3.235 31.699 13 AA_C32C33:G11G12_AA A 32 ? A 12 ? A 33 ? A 11 ? 1 A C 33 1_555 A G 11 1_555 A U 34 1_555 A A 10 1_555 -0.524 -1.894 3.162 -1.870 9.348 28.753 -5.299 0.669 2.467 18.204 3.642 30.260 14 AA_C33U34:A10G11_AA A 33 ? A 11 ? A 34 ? A 10 ? 1 A U 34 1_555 A A 10 1_555 A U 35 1_555 A A 9 1_555 0.220 -1.627 3.055 -1.980 12.389 19.849 -7.328 -1.072 1.722 32.123 5.135 23.448 15 AA_U34U35:A9A10_AA A 34 ? A 10 ? A 35 ? A 9 ? 1 A U 35 1_555 A A 9 1_555 A G 36 1_555 A G 31 1_555 2.828 -4.231 2.315 25.493 8.980 113.419 -2.573 -1.468 2.480 5.329 -15.130 115.490 16 AA_U35G36:G31A9_AA A 35 ? A 9 ? A 36 ? A 31 ? 1 A C 40 1_555 A G 47 1_555 A C 41 1_555 A G 46 1_555 -0.448 -2.389 3.403 0.161 6.039 29.214 -5.860 0.902 2.860 11.814 -0.314 29.819 17 AA_C40C41:G46G47_AA A 40 ? A 47 ? A 41 ? A 46 ? 1 A C 41 1_555 A G 46 1_555 A G 42 1_555 A A 45 1_555 -4.361 -1.625 2.957 0.406 10.942 53.826 -2.323 4.755 2.577 11.947 -0.444 54.847 18 AA_C41G42:A45G46_AA A 41 ? A 46 ? A 42 ? A 45 ? # _atom_sites.entry_id 3E5C _atom_sites.fract_transf_matrix[1][1] 0.010224 _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] 0.010224 _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] 0.011476 _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 S SR # loop_