data_485D # _entry.id 485D # _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 485D pdb_0000485d 10.2210/pdb485d/pdb NDB AR0019 ? ? RCSB RCSB001324 ? ? WWPDB D_1000001324 ? ? # 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 1999-12-18 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_keywords 5 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_keywords.text' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 485D _pdbx_database_status.recvd_initial_deposition_date 1999-08-13 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _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_ _audit_author.name _audit_author.pdbx_ordinal 'Masquida, B.' 1 'Sauter, C.' 2 'Westhof, E.' 3 # _citation.id primary _citation.title 'A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.' _citation.journal_abbrev RNA _citation.journal_volume 5 _citation.page_first 1384 _citation.page_last 1395 _citation.year 1999 _citation.journal_id_ASTM RNARFU _citation.country UK _citation.journal_id_ISSN 1355-8382 _citation.journal_id_CSD 2122 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10573129 _citation.pdbx_database_id_DOI 10.1017/S1355838299991173 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Masquida, B.' 1 ? primary 'Sauter, C.' 2 ? primary 'Westhof, E.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "RNA/DNA(5'-R(*CP*GP*UP*GP*AP*UP*CP*GP)-D(*C)-3')" 2815.743 2 ? ? ? ? 2 non-polymer syn 'SULFATE ION' 96.063 1 ? ? ? ? 3 water nat water 18.015 84 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)GUGAUCG(DC)' _entity_poly.pdbx_seq_one_letter_code_can CGUGAUCGC _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 'SULFATE ION' SO4 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 G n 1 3 U n 1 4 G n 1 5 A n 1 6 U n 1 7 C n 1 8 G n 1 9 DC n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 DC 1 1 1 DC C A . n A 1 2 G 2 2 2 G G A . n A 1 3 U 3 3 3 U U A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A 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 G 8 8 8 G G A . n A 1 9 DC 9 9 9 DC C A . n B 1 1 DC 1 10 10 DC C B . n B 1 2 G 2 11 11 G G B . n B 1 3 U 3 12 12 U U B . n B 1 4 G 4 13 13 G G B . n B 1 5 A 5 14 14 A A B . n B 1 6 U 6 15 15 U U B . n B 1 7 C 7 16 16 C C B . n B 1 8 G 8 17 17 G G B . n B 1 9 DC 9 18 18 DC 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 SO4 1 19 19 SO4 SO4 B . D 3 HOH 1 101 101 HOH HOH A . D 3 HOH 2 105 105 HOH HOH A . D 3 HOH 3 108 108 HOH HOH A . D 3 HOH 4 113 113 HOH HOH A . D 3 HOH 5 114 114 HOH HOH A . D 3 HOH 6 116 116 HOH HOH A . D 3 HOH 7 118 118 HOH HOH A . D 3 HOH 8 119 119 HOH HOH A . D 3 HOH 9 120 120 HOH HOH A . D 3 HOH 10 123 123 HOH HOH A . D 3 HOH 11 124 124 HOH HOH A . D 3 HOH 12 129 129 HOH HOH A . D 3 HOH 13 130 130 HOH HOH A . D 3 HOH 14 131 131 HOH HOH A . D 3 HOH 15 133 133 HOH HOH A . D 3 HOH 16 134 134 HOH HOH A . D 3 HOH 17 135 135 HOH HOH A . D 3 HOH 18 137 137 HOH HOH A . D 3 HOH 19 140 140 HOH HOH A . D 3 HOH 20 141 141 HOH HOH A . D 3 HOH 21 142 142 HOH HOH A . D 3 HOH 22 143 143 HOH HOH A . D 3 HOH 23 146 146 HOH HOH A . D 3 HOH 24 147 147 HOH HOH A . D 3 HOH 25 148 148 HOH HOH A . D 3 HOH 26 149 149 HOH HOH A . D 3 HOH 27 151 151 HOH HOH A . D 3 HOH 28 153 153 HOH HOH A . D 3 HOH 29 155 155 HOH HOH A . D 3 HOH 30 156 156 HOH HOH A . D 3 HOH 31 157 157 HOH HOH A . D 3 HOH 32 158 158 HOH HOH A . D 3 HOH 33 160 160 HOH HOH A . D 3 HOH 34 161 161 HOH HOH A . D 3 HOH 35 163 163 HOH HOH A . D 3 HOH 36 165 165 HOH HOH A . D 3 HOH 37 166 166 HOH HOH A . D 3 HOH 38 167 167 HOH HOH A . D 3 HOH 39 168 168 HOH HOH A . D 3 HOH 40 170 170 HOH HOH A . D 3 HOH 41 171 171 HOH HOH A . D 3 HOH 42 173 173 HOH HOH A . D 3 HOH 43 178 178 HOH HOH A . D 3 HOH 44 181 181 HOH HOH A . D 3 HOH 45 184 184 HOH HOH A . E 3 HOH 1 102 102 HOH HOH B . E 3 HOH 2 103 103 HOH HOH B . E 3 HOH 3 104 104 HOH HOH B . E 3 HOH 4 106 106 HOH HOH B . E 3 HOH 5 107 107 HOH HOH B . E 3 HOH 6 109 109 HOH HOH B . E 3 HOH 7 110 110 HOH HOH B . E 3 HOH 8 111 111 HOH HOH B . E 3 HOH 9 112 112 HOH HOH B . E 3 HOH 10 115 115 HOH HOH B . E 3 HOH 11 117 117 HOH HOH B . E 3 HOH 12 121 121 HOH HOH B . E 3 HOH 13 122 122 HOH HOH B . E 3 HOH 14 125 125 HOH HOH B . E 3 HOH 15 126 126 HOH HOH B . E 3 HOH 16 127 127 HOH HOH B . E 3 HOH 17 128 128 HOH HOH B . E 3 HOH 18 132 132 HOH HOH B . E 3 HOH 19 136 136 HOH HOH B . E 3 HOH 20 138 138 HOH HOH B . E 3 HOH 21 139 139 HOH HOH B . E 3 HOH 22 144 144 HOH HOH B . E 3 HOH 23 145 145 HOH HOH B . E 3 HOH 24 150 150 HOH HOH B . E 3 HOH 25 152 152 HOH HOH B . E 3 HOH 26 154 154 HOH HOH B . E 3 HOH 27 159 159 HOH HOH B . E 3 HOH 28 162 162 HOH HOH B . E 3 HOH 29 164 164 HOH HOH B . E 3 HOH 30 169 169 HOH HOH B . E 3 HOH 31 172 172 HOH HOH B . E 3 HOH 32 174 174 HOH HOH B . E 3 HOH 33 175 175 HOH HOH B . E 3 HOH 34 176 176 HOH HOH B . E 3 HOH 35 177 177 HOH HOH B . E 3 HOH 36 179 179 HOH HOH B . E 3 HOH 37 180 180 HOH HOH B . E 3 HOH 38 182 182 HOH HOH B . E 3 HOH 39 183 183 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A DC 1 ? "O5'" ? A DC 1 "O5'" 2 1 Y 1 A DC 1 ? "C5'" ? A DC 1 "C5'" 3 1 Y 1 A DC 1 ? "C4'" ? A DC 1 "C4'" 4 1 Y 1 A DC 1 ? "O4'" ? A DC 1 "O4'" 5 1 Y 1 A DC 1 ? "C3'" ? A DC 1 "C3'" 6 1 Y 1 A DC 1 ? "C2'" ? A DC 1 "C2'" 7 1 Y 1 A DC 1 ? "C1'" ? A DC 1 "C1'" 8 1 Y 1 A DC 1 ? N1 ? A DC 1 N1 9 1 Y 1 A DC 1 ? C2 ? A DC 1 C2 10 1 Y 1 A DC 1 ? O2 ? A DC 1 O2 11 1 Y 1 A DC 1 ? N3 ? A DC 1 N3 12 1 Y 1 A DC 1 ? C4 ? A DC 1 C4 13 1 Y 1 A DC 1 ? N4 ? A DC 1 N4 14 1 Y 1 A DC 1 ? C5 ? A DC 1 C5 15 1 Y 1 A DC 1 ? C6 ? A DC 1 C6 16 1 Y 1 B DC 10 ? "O5'" ? B DC 1 "O5'" 17 1 Y 1 B DC 10 ? "C5'" ? B DC 1 "C5'" 18 1 Y 1 B DC 10 ? "C4'" ? B DC 1 "C4'" 19 1 Y 1 B DC 10 ? "O4'" ? B DC 1 "O4'" 20 1 Y 1 B DC 10 ? "C3'" ? B DC 1 "C3'" 21 1 Y 1 B DC 10 ? "C2'" ? B DC 1 "C2'" 22 1 Y 1 B DC 10 ? "C1'" ? B DC 1 "C1'" 23 1 Y 1 B DC 10 ? N1 ? B DC 1 N1 24 1 Y 1 B DC 10 ? C2 ? B DC 1 C2 25 1 Y 1 B DC 10 ? O2 ? B DC 1 O2 26 1 Y 1 B DC 10 ? N3 ? B DC 1 N3 27 1 Y 1 B DC 10 ? C4 ? B DC 1 C4 28 1 Y 1 B DC 10 ? N4 ? B DC 1 N4 29 1 Y 1 B DC 10 ? C5 ? B DC 1 C5 30 1 Y 1 B DC 10 ? C6 ? B DC 1 C6 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 SHELXL-97 refinement . ? 4 # _cell.entry_id 485D _cell.length_a 39.958 _cell.length_b 39.958 _cell.length_c 67.445 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _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 485D _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? # _exptl.entry_id 485D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 33.15 _exptl_crystal.density_Matthews 1.84 _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 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;2.2-2.6 M AMMONIUM SULFATE, 5-50 MM MAGNESIUM SULFATE, 50 MM SODIUM CACODYLATE, 1MM SPERMINE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 310K ; _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 '(NH4)2SO4' ? ? ? 1 2 1 MGSO4 ? ? ? 1 3 1 'SODIUM CACODYLATE,' ? ? ? 1 4 1 SPERMINE ? ? ? 1 5 2 '(NH4)2SO4' ? ? ? 1 6 2 MGSO4 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9343 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength 0.9343 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 485D _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 0.97 _reflns.number_obs 23838 _reflns.number_all 23838 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.041 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.91 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 0.97 _reflns_shell.d_res_low 0.99 _reflns_shell.percent_possible_all 99.9 _reflns_shell.Rmerge_I_obs 0.446 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 2.63 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 485D _refine.ls_number_reflns_obs 23838 _refine.ls_number_reflns_all 23838 _refine.pdbx_ls_sigma_I 0.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.0 _refine.ls_d_res_high 0.97 _refine.ls_percent_reflns_obs 99.8 _refine.ls_R_factor_obs 0.1503 _refine.ls_R_factor_all 0.1503 _refine.ls_R_factor_R_work 0.1487 _refine.ls_R_factor_R_free 0.1954 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5 _refine.ls_number_reflns_R_free 1292 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details 'THIN SHELLS' _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_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_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 342 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 84 _refine_hist.number_atoms_total 431 _refine_hist.d_res_high 0.97 _refine_hist.d_res_low 20.0 # 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 s_bond_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.018 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 485D _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 485D _struct.title 'A SULFATE POCKET FORMED BY THREE GOU PAIRS IN THE STRUCTURE OF A NONAMERIC RNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 485D _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'RNA, DNA/RNA HYBRID, SULFATE ION, DNA-RNA HYBRID complex, DNA-RNA HYBRID' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 485D _struct_ref.pdbx_db_accession 485D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 485D A 1 ? 9 ? 485D 1 ? 9 ? 1 9 2 1 485D B 1 ? 9 ? 485D 10 ? 18 ? 10 18 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # _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 hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A G 2 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B DC 9 O2 ? ? A G 2 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B DC 9 N4 ? ? A G 2 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 3 N3 ? ? ? 1_555 B G 8 O6 ? ? A U 3 B G 17 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog5 hydrog ? ? A U 3 O2 ? ? ? 1_555 B G 8 N1 ? ? A U 3 B G 17 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog6 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 4 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 4 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 4 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 5 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 5 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 6 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 6 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 7 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 7 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 7 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 8 N1 ? ? ? 1_555 B U 3 O2 ? ? A G 8 B U 12 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog17 hydrog ? ? A G 8 O6 ? ? ? 1_555 B U 3 N3 ? ? A G 8 B U 12 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 2 N1 ? ? A DC 9 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 2 O6 ? ? A DC 9 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 2 N2 ? ? A DC 9 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id SO4 _struct_site.pdbx_auth_seq_id 19 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 12 _struct_site.details 'BINDING SITE FOR RESIDUE SO4 B 19' # 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 12 G B 8 ? G B 17 . ? 1_555 ? 2 AC1 12 G B 8 ? G B 17 . ? 3_665 ? 3 AC1 12 G B 8 ? G B 17 . ? 2_655 ? 4 AC1 12 DC B 9 ? DC B 18 . ? 1_555 ? 5 AC1 12 DC B 9 ? DC B 18 . ? 3_665 ? 6 AC1 12 DC B 9 ? DC B 18 . ? 2_655 ? 7 AC1 12 HOH E . ? HOH B 103 . ? 3_665 ? 8 AC1 12 HOH E . ? HOH B 103 . ? 2_655 ? 9 AC1 12 HOH E . ? HOH B 103 . ? 1_555 ? 10 AC1 12 HOH E . ? HOH B 145 . ? 1_555 ? 11 AC1 12 HOH E . ? HOH B 145 . ? 3_665 ? 12 AC1 12 HOH E . ? HOH B 145 . ? 2_655 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DC 1 ? ? P A G 2 ? ? 1.482 1.607 -0.125 0.012 Y 2 1 "C2'" A G 2 ? ? "C1'" A G 2 ? ? 1.467 1.526 -0.059 0.008 N 3 1 "O4'" A G 2 ? ? "C1'" A G 2 ? ? 1.503 1.415 0.088 0.012 N 4 1 "C2'" A U 3 ? ? "C1'" A U 3 ? ? 1.468 1.526 -0.058 0.008 N 5 1 "C2'" A G 4 ? ? "C1'" A G 4 ? ? 1.459 1.526 -0.067 0.008 N 6 1 "C2'" A A 5 ? ? "C1'" A A 5 ? ? 1.477 1.526 -0.049 0.008 N 7 1 N1 A A 5 ? ? C2 A A 5 ? ? 1.262 1.339 -0.077 0.009 N 8 1 N3 A A 5 ? ? C4 A A 5 ? ? 1.290 1.344 -0.054 0.006 N 9 1 C6 A A 5 ? ? N1 A A 5 ? ? 1.399 1.351 0.048 0.007 N 10 1 C5 A A 5 ? ? N7 A A 5 ? ? 1.343 1.388 -0.045 0.006 N 11 1 N7 A A 5 ? ? C8 A A 5 ? ? 1.355 1.311 0.044 0.007 N 12 1 "C2'" A U 6 ? ? "C1'" A U 6 ? ? 1.458 1.526 -0.068 0.008 N 13 1 "O4'" A U 6 ? ? "C1'" A U 6 ? ? 1.490 1.415 0.075 0.012 N 14 1 "C2'" A G 8 ? ? "C1'" A G 8 ? ? 1.470 1.526 -0.056 0.008 N 15 1 "O3'" B DC 10 ? ? P B G 11 ? ? 1.489 1.607 -0.118 0.012 Y 16 1 "C2'" B G 11 ? ? "C1'" B G 11 ? ? 1.465 1.526 -0.061 0.008 N 17 1 "C2'" B U 12 ? ? "C1'" B U 12 ? ? 1.459 1.526 -0.067 0.008 N 18 1 N1 B A 14 ? ? C2 B A 14 ? ? 1.265 1.339 -0.074 0.009 N 19 1 N3 B A 14 ? ? C4 B A 14 ? ? 1.281 1.344 -0.063 0.006 N 20 1 C5 B A 14 ? ? N7 B A 14 ? ? 1.328 1.388 -0.060 0.006 N 21 1 "C2'" B G 17 ? ? "C1'" B G 17 ? ? 1.451 1.526 -0.075 0.008 N 22 1 C4 B DC 18 ? ? C5 B DC 18 ? ? 1.475 1.425 0.050 0.008 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N9 A G 2 ? ? "C1'" A G 2 ? ? "C2'" A G 2 ? ? 121.85 114.00 7.85 1.30 N 2 1 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 101.78 108.20 -6.42 0.80 N 3 1 C5 A U 3 ? ? C6 A U 3 ? ? N1 A U 3 ? ? 125.82 122.70 3.12 0.50 N 4 1 N1 A G 4 ? ? C6 A G 4 ? ? O6 A G 4 ? ? 115.96 119.90 -3.94 0.60 N 5 1 C4 A A 5 ? ? C5 A A 5 ? ? N7 A A 5 ? ? 114.02 110.70 3.32 0.50 N 6 1 N7 A A 5 ? ? C8 A A 5 ? ? N9 A A 5 ? ? 110.75 113.80 -3.05 0.50 N 7 1 N9 A A 5 ? ? C4 A A 5 ? ? C5 A A 5 ? ? 103.31 105.80 -2.49 0.40 N 8 1 "C1'" A C 7 ? ? "O4'" A C 7 ? ? "C4'" A C 7 ? ? 105.45 109.70 -4.25 0.70 N 9 1 C2 A C 7 ? ? N3 A C 7 ? ? C4 A C 7 ? ? 116.41 119.90 -3.49 0.50 N 10 1 P A G 8 ? ? "O5'" A G 8 ? ? "C5'" A G 8 ? ? 137.93 120.90 17.03 1.60 N 11 1 N1 A G 8 ? ? C6 A G 8 ? ? O6 A G 8 ? ? 116.03 119.90 -3.87 0.60 N 12 1 "O4'" A DC 9 ? ? "C4'" A DC 9 ? ? "C3'" A DC 9 ? ? 100.59 104.50 -3.91 0.40 N 13 1 OP1 B G 11 ? ? P B G 11 ? ? OP2 B G 11 ? ? 108.70 119.60 -10.90 1.50 N 14 1 N1 B U 12 ? ? C2 B U 12 ? ? O2 B U 12 ? ? 117.00 122.80 -5.80 0.70 N 15 1 N3 B U 12 ? ? C2 B U 12 ? ? O2 B U 12 ? ? 127.87 122.20 5.67 0.70 N 16 1 C4 B A 14 ? ? C5 B A 14 ? ? N7 B A 14 ? ? 113.71 110.70 3.01 0.50 N 17 1 N9 B A 14 ? ? C4 B A 14 ? ? C5 B A 14 ? ? 102.78 105.80 -3.02 0.40 N 18 1 C5 B U 15 ? ? C6 B U 15 ? ? N1 B U 15 ? ? 125.80 122.70 3.10 0.50 N # 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 B SO4 19 ? C SO4 . 2 1 A HOH 101 ? D HOH . 3 1 A HOH 123 ? D HOH . 4 1 A HOH 133 ? D HOH . 5 1 A HOH 153 ? D HOH . 6 1 B HOH 102 ? E HOH . 7 1 B HOH 104 ? E HOH . 8 1 B HOH 107 ? E HOH . # 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 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 SO4 S S N N 148 SO4 O1 O N N 149 SO4 O2 O N N 150 SO4 O3 O N N 151 SO4 O4 O N N 152 U OP3 O N N 153 U P P N N 154 U OP1 O N N 155 U OP2 O N N 156 U "O5'" O N N 157 U "C5'" C N N 158 U "C4'" C N R 159 U "O4'" O N N 160 U "C3'" C N S 161 U "O3'" O N N 162 U "C2'" C N R 163 U "O2'" O N N 164 U "C1'" C N R 165 U N1 N N N 166 U C2 C N N 167 U O2 O N N 168 U N3 N N N 169 U C4 C N N 170 U O4 O N N 171 U C5 C N N 172 U C6 C N N 173 U HOP3 H N N 174 U HOP2 H N N 175 U "H5'" H N N 176 U "H5''" H N N 177 U "H4'" H N N 178 U "H3'" H N N 179 U "HO3'" H N N 180 U "H2'" H N N 181 U "HO2'" H N N 182 U "H1'" H N N 183 U H3 H N N 184 U H5 H N N 185 U H6 H N N 186 # 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 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 SO4 S O1 doub N N 153 SO4 S O2 doub N N 154 SO4 S O3 sing N N 155 SO4 S O4 sing N N 156 U OP3 P sing N N 157 U OP3 HOP3 sing N N 158 U P OP1 doub N N 159 U P OP2 sing N N 160 U P "O5'" sing N N 161 U OP2 HOP2 sing N N 162 U "O5'" "C5'" sing N N 163 U "C5'" "C4'" sing N N 164 U "C5'" "H5'" sing N N 165 U "C5'" "H5''" sing N N 166 U "C4'" "O4'" sing N N 167 U "C4'" "C3'" sing N N 168 U "C4'" "H4'" sing N N 169 U "O4'" "C1'" sing N N 170 U "C3'" "O3'" sing N N 171 U "C3'" "C2'" sing N N 172 U "C3'" "H3'" sing N N 173 U "O3'" "HO3'" sing N N 174 U "C2'" "O2'" sing N N 175 U "C2'" "C1'" sing N N 176 U "C2'" "H2'" sing N N 177 U "O2'" "HO2'" sing N N 178 U "C1'" N1 sing N N 179 U "C1'" "H1'" sing N N 180 U N1 C2 sing N N 181 U N1 C6 sing N N 182 U C2 O2 doub N N 183 U C2 N3 sing N N 184 U N3 C4 sing N N 185 U N3 H3 sing N N 186 U C4 O4 doub N N 187 U C4 C5 sing N N 188 U C5 C6 doub N N 189 U C5 H5 sing N N 190 U C6 H6 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 485D 'a-form double helix' 485D 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 2 1_555 B DC 9 1_555 -0.165 -0.142 0.139 -2.685 -10.134 -3.162 1 A_G2:DC18_B A 2 ? B 18 ? 19 1 1 A U 3 1_555 B G 8 1_555 2.360 -0.604 0.077 1.073 -12.165 -0.536 2 A_U3:G17_B A 3 ? B 17 ? 28 ? 1 A G 4 1_555 B C 7 1_555 -0.159 -0.032 -0.171 -6.524 -11.462 2.424 3 A_G4:C16_B A 4 ? B 16 ? 19 1 1 A A 5 1_555 B U 6 1_555 -0.016 -0.048 0.069 -0.561 -6.370 -2.573 4 A_A5:U15_B A 5 ? B 15 ? 20 1 1 A U 6 1_555 B A 5 1_555 -0.127 -0.091 0.010 1.278 -14.518 0.210 5 A_U6:A14_B A 6 ? B 14 ? 20 1 1 A C 7 1_555 B G 4 1_555 0.250 -0.193 -0.056 4.087 -5.720 -3.084 6 A_C7:G13_B A 7 ? B 13 ? 19 1 1 A G 8 1_555 B U 3 1_555 -2.340 -0.418 -0.097 -2.063 -10.336 3.240 7 A_G8:U12_B A 8 ? B 12 ? 28 ? 1 A DC 9 1_555 B G 2 1_555 0.233 -0.082 0.001 -2.860 -5.766 0.599 8 A_DC9:G11_B A 9 ? B 11 ? 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 2 1_555 B DC 9 1_555 A U 3 1_555 B G 8 1_555 -0.006 -1.221 3.215 0.814 4.917 42.682 -2.136 0.086 3.062 6.727 -1.114 42.959 1 AA_G2U3:G17DC18_BB A 2 ? B 18 ? A 3 ? B 17 ? 1 A U 3 1_555 B G 8 1_555 A G 4 1_555 B C 7 1_555 0.703 -1.957 3.286 5.152 10.741 25.119 -6.430 -0.337 2.362 23.110 -11.085 27.759 2 AA_U3G4:C16G17_BB A 3 ? B 17 ? A 4 ? B 16 ? 1 A G 4 1_555 B C 7 1_555 A A 5 1_555 B U 6 1_555 -0.525 -2.056 3.138 -1.849 4.230 25.530 -5.650 0.702 2.797 9.474 4.140 25.937 3 AA_G4A5:U15C16_BB A 4 ? B 16 ? A 5 ? B 15 ? 1 A A 5 1_555 B U 6 1_555 A U 6 1_555 B A 5 1_555 -0.124 -1.775 3.242 -1.227 3.444 31.917 -3.803 0.012 3.042 6.236 2.223 32.120 4 AA_A5U6:A14U15_BB A 5 ? B 15 ? A 6 ? B 14 ? 1 A U 6 1_555 B A 5 1_555 A C 7 1_555 B G 4 1_555 -0.589 -1.371 3.239 -1.704 6.233 32.127 -3.458 0.764 2.954 11.122 3.041 32.754 5 AA_U6C7:G13A14_BB A 6 ? B 14 ? A 7 ? B 13 ? 1 A C 7 1_555 B G 4 1_555 A G 8 1_555 B U 3 1_555 1.689 -1.988 3.341 0.534 10.209 20.134 -8.393 -4.144 2.135 27.063 -1.415 22.557 6 AA_C7G8:U12G13_BB A 7 ? B 13 ? A 8 ? B 12 ? 1 A G 8 1_555 B U 3 1_555 A DC 9 1_555 B G 2 1_555 -0.180 -1.791 3.350 -0.229 3.228 43.076 -2.751 0.222 3.214 4.388 0.312 43.191 7 AA_G8DC9:G11U12_BB A 8 ? B 12 ? A 9 ? B 11 ? # _atom_sites.entry_id 485D _atom_sites.fract_transf_matrix[1][1] 0.025026 _atom_sites.fract_transf_matrix[1][2] 0.014449 _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] 0.028898 _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] 0.014827 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P S # loop_