data_4OQU # _entry.id 4OQU # _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 4OQU pdb_00004oqu 10.2210/pdb4oqu/pdb NDB NA2938 ? ? RCSB RCSB084835 ? ? WWPDB D_1000084835 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2014-06-04 2 'Structure model' 1 1 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4OQU _pdbx_database_status.recvd_initial_deposition_date 2014-02-10 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Trausch, J.J.' 1 'Reyes, F.E.' 2 'Edwards, A.L.' 3 'Batey, R.T.' 4 # _citation.id primary _citation.title 'Structural basis for diversity in the SAM clan of riboswitches.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 111 _citation.page_first 6624 _citation.page_last 6629 _citation.year 2014 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24753586 _citation.pdbx_database_id_DOI 10.1073/pnas.1312918111 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Trausch, J.J.' 1 ? primary 'Xu, Z.' 2 ? primary 'Edwards, A.L.' 3 ? primary 'Reyes, F.E.' 4 ? primary 'Ross, P.E.' 5 ? primary 'Knight, R.' 6 ? primary 'Batey, R.T.' 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 'SAM-I/IV riboswitch' 31622.029 1 ? ? ? ? 2 non-polymer syn S-ADENOSYLMETHIONINE 398.437 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 5 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GGAUCACGAGGGGGAGACCCCGGCAACCUGGGACGGACACCCAAGGUGCUCACACCGGAGACGGUGGAUCCGGCCCGAGA GGGCAACGAAGGUCCGA ; _entity_poly.pdbx_seq_one_letter_code_can ;GGAUCACGAGGGGGAGACCCCGGCAACCUGGGACGGACACCCAAGGUGCUCACACCGGAGACGGUGGAUCCGGCCCGAGA GGGCAACGAAGGUCCGA ; _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 S-ADENOSYLMETHIONINE SAM 3 'MAGNESIUM ION' MG # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 A n 1 4 U n 1 5 C n 1 6 A n 1 7 C n 1 8 G n 1 9 A n 1 10 G n 1 11 G n 1 12 G n 1 13 G n 1 14 G n 1 15 A n 1 16 G n 1 17 A n 1 18 C n 1 19 C n 1 20 C n 1 21 C n 1 22 G n 1 23 G n 1 24 C n 1 25 A n 1 26 A n 1 27 C n 1 28 C n 1 29 U n 1 30 G n 1 31 G n 1 32 G n 1 33 A n 1 34 C n 1 35 G n 1 36 G n 1 37 A n 1 38 C n 1 39 A n 1 40 C n 1 41 C n 1 42 C n 1 43 A n 1 44 A n 1 45 G n 1 46 G n 1 47 U n 1 48 G n 1 49 C n 1 50 U n 1 51 C n 1 52 A n 1 53 C n 1 54 A n 1 55 C n 1 56 C n 1 57 G n 1 58 G n 1 59 A n 1 60 G n 1 61 A n 1 62 C n 1 63 G n 1 64 G n 1 65 U n 1 66 G n 1 67 G n 1 68 A n 1 69 U n 1 70 C n 1 71 C n 1 72 G n 1 73 G n 1 74 C n 1 75 C n 1 76 C n 1 77 G n 1 78 A n 1 79 G n 1 80 A n 1 81 G n 1 82 G n 1 83 G n 1 84 C n 1 85 A n 1 86 A n 1 87 C n 1 88 G n 1 89 A n 1 90 A n 1 91 G n 1 92 G n 1 93 U n 1 94 C n 1 95 C n 1 96 G n 1 97 A 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 'T7 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 SAM non-polymer . S-ADENOSYLMETHIONINE ? 'C15 H22 N6 O5 S' 398.437 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 U 4 4 4 U U A . n A 1 5 C 5 5 5 C C A . n A 1 6 A 6 6 6 A A 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 A 9 9 9 A A A . n A 1 10 G 10 10 10 G G A . n A 1 11 G 11 11 11 G G A . n A 1 12 G 12 12 12 G G A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 A 15 15 15 A A A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 C 18 18 18 C C A . n A 1 19 C 19 19 19 C C A . n A 1 20 C 20 20 20 C C A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 G 23 23 23 G G A . n A 1 24 C 24 24 24 C C A . n A 1 25 A 25 25 25 A A A . n A 1 26 A 26 26 26 A A A . n A 1 27 C 27 27 27 C C A . n A 1 28 C 28 28 28 C C A . n A 1 29 U 29 29 29 U U A . n A 1 30 G 30 30 30 G G A . n A 1 31 G 31 31 31 G G A . n A 1 32 G 32 32 32 G G A . n A 1 33 A 33 33 33 A A A . n A 1 34 C 34 34 34 C C A . n A 1 35 G 35 35 35 G G A . n A 1 36 G 36 36 36 G G A . n A 1 37 A 37 37 37 A A A . n A 1 38 C 38 38 38 C C A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 C 41 41 41 C C A . n A 1 42 C 42 42 42 C C A . n A 1 43 A 43 43 43 A A A . n A 1 44 A 44 44 44 A A A . n A 1 45 G 45 45 45 G G A . n A 1 46 G 46 46 46 G G A . n A 1 47 U 47 47 47 U U A . n A 1 48 G 48 48 48 G G A . n A 1 49 C 49 49 49 C C A . n A 1 50 U 50 50 50 U U A . n A 1 51 C 51 51 51 C C A . n A 1 52 A 52 52 52 A A A . n A 1 53 C 53 53 53 C C A . n A 1 54 A 54 54 54 A A A . n A 1 55 C 55 55 55 C C A . n A 1 56 C 56 56 56 C C A . n A 1 57 G 57 57 57 G G A . n A 1 58 G 58 58 58 G G A . n A 1 59 A 59 59 59 A A A . n A 1 60 G 60 60 60 G G A . n A 1 61 A 61 61 61 A A A . n A 1 62 C 62 62 62 C C A . n A 1 63 G 63 63 63 G G A . n A 1 64 G 64 64 64 G G A . n A 1 65 U 65 65 65 U U A . n A 1 66 G 66 66 66 G G A . n A 1 67 G 67 67 67 G G A . n A 1 68 A 68 68 68 A A A . n A 1 69 U 69 69 69 U U A . n A 1 70 C 70 70 70 C C A . n A 1 71 C 71 71 71 C C A . n A 1 72 G 72 72 72 G G A . n A 1 73 G 73 73 73 G G A . n A 1 74 C 74 74 74 C C A . n A 1 75 C 75 75 75 C C A . n A 1 76 C 76 76 76 C C A . n A 1 77 G 77 77 77 G G A . n A 1 78 A 78 78 78 A A A . n A 1 79 G 79 79 79 G G A . n A 1 80 A 80 80 80 A A A . n A 1 81 G 81 81 81 G G A . n A 1 82 G 82 82 82 G G A . n A 1 83 G 83 83 83 G G A . n A 1 84 C 84 84 84 C C A . n A 1 85 A 85 85 85 A A A . n A 1 86 A 86 86 86 A A A . n A 1 87 C 87 87 87 C C A . n A 1 88 G 88 88 88 G G A . n A 1 89 A 89 89 89 A A A . n A 1 90 A 90 90 90 A A A . n A 1 91 G 91 91 91 G G A . n A 1 92 G 92 92 92 G G A . n A 1 93 U 93 93 93 U U A . n A 1 94 C 94 94 94 C C A . n A 1 95 C 95 95 95 C C A . n A 1 96 G 96 96 96 G G A . n A 1 97 A 97 97 97 A A 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 SAM 1 101 101 SAM SAM A . C 3 MG 1 102 201 MG MG A . D 3 MG 1 103 202 MG MG A . E 3 MG 1 104 203 MG MG A . F 3 MG 1 105 204 MG MG A . G 3 MG 1 106 205 MG MG A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal BOS 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.8.4_1496)' ? 3 CrystalClear 'data reduction' . ? 4 CrystalClear 'data scaling' . ? 5 # _cell.entry_id 4OQU _cell.length_a 127.269 _cell.length_b 127.269 _cell.length_c 181.609 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 4OQU _symmetry.space_group_name_H-M 'P 64 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4OQU _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _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 303.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 303.15K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2014-01-17 _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 'Double crystal, Si(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9999 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9999 # _reflns.entry_id 4OQU _reflns.observed_criterion_sigma_I 1.9 _reflns.observed_criterion_sigma_F 1.9 _reflns.d_resolution_low 41.66 _reflns.d_resolution_high 3.20 _reflns.number_obs 14916 _reflns.number_all 14952 _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 3.20 _reflns_shell.d_res_low 3.31 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4OQU _refine.ls_number_reflns_obs 14854 _refine.ls_number_reflns_all 14854 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 31.408 _refine.ls_d_res_high 3.200 _refine.ls_percent_reflns_obs 99.42 _refine.ls_R_factor_obs 0.1987 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1957 _refine.ls_R_factor_R_free 0.2263 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.00 _refine.ls_number_reflns_R_free 1486 _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 ? _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details 10% _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.41 _refine.pdbx_overall_phase_error 26.16 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_refine_id 'X-RAY DIFFRACTION' _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 2100 _refine_hist.pdbx_number_atoms_ligand 32 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 2132 _refine_hist.d_res_high 3.200 _refine_hist.d_res_low 31.408 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.006 ? ? 2383 ? 'X-RAY DIFFRACTION' f_angle_d 1.252 ? ? 3718 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 12.884 ? ? 1162 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.052 ? ? 491 ? 'X-RAY DIFFRACTION' f_plane_restr 0.007 ? ? 99 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _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 . 3.2000 3.3032 1183 0.3547 100.00 0.3982 . . 132 . . . . 'X-RAY DIFFRACTION' . 3.3032 3.4211 1186 0.3178 99.00 0.3227 . . 129 . . . . 'X-RAY DIFFRACTION' . 3.4211 3.5579 1194 0.2963 99.00 0.3001 . . 133 . . . . 'X-RAY DIFFRACTION' . 3.5579 3.7196 1175 0.2464 99.00 0.2844 . . 132 . . . . 'X-RAY DIFFRACTION' . 3.7196 3.9154 1198 0.2278 100.00 0.2729 . . 133 . . . . 'X-RAY DIFFRACTION' . 3.9154 4.1602 1195 0.2140 100.00 0.2242 . . 133 . . . . 'X-RAY DIFFRACTION' . 4.1602 4.4805 1210 0.1983 100.00 0.2318 . . 135 . . . . 'X-RAY DIFFRACTION' . 4.4805 4.9299 1225 0.1646 100.00 0.2461 . . 135 . . . . 'X-RAY DIFFRACTION' . 4.9299 5.6397 1223 0.1485 100.00 0.1730 . . 137 . . . . 'X-RAY DIFFRACTION' . 5.6397 7.0919 1260 0.1654 100.00 0.1888 . . 140 . . . . 'X-RAY DIFFRACTION' . 7.0919 31.4093 1319 0.1820 98.00 0.2089 . . 147 . . . . 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4OQU _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 4OQU _struct.title 'Structure of the SAM-I/IV riboswitch (env87(deltaU92))' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4OQU _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'riboswitch, aptamer, pseudoknot, regulation, S-adenosylmethionine, 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 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4OQU _struct_ref.pdbx_db_accession 4OQU _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ;GGAUCACGAGGGGGAGACCCCGGCAACCUGGGACGGACACCCAAGGUGCUCACACCGGAGACGGUGGAUCCGGCCCGAGA GGGCAACGAAGGUCCGA ; _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4OQU _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 97 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4OQU _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 97 _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 97 # _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 # _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 metalc1 metalc ? ? A A 33 OP2 ? ? ? 1_555 G MG . MG ? ? A A 33 A MG 106 1_555 ? ? ? ? ? ? ? 2.891 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 71 N3 ? ? A G 1 A C 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 71 O2 ? ? A G 1 A C 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 71 N4 ? ? A G 1 A C 71 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 70 N3 ? ? A G 2 A C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 70 O2 ? ? A G 2 A C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 70 N4 ? ? A G 2 A C 70 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 69 N3 ? ? A A 3 A U 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 69 O4 ? ? A A 3 A U 69 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 68 N1 ? ? A U 4 A A 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 68 N6 ? ? A U 4 A A 68 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 67 N1 ? ? A C 5 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 67 O6 ? ? A C 5 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 67 N2 ? ? A C 5 A G 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 24 O2 ? ? A G 8 A C 24 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog15 hydrog ? ? A A 9 N3 ? ? ? 1_555 A G 23 N2 ? ? A A 9 A G 23 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog16 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 10 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 10 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 10 A C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 20 N3 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 20 O2 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 20 N4 ? ? A G 11 A C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 19 N3 ? ? A G 12 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 19 O2 ? ? A G 12 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 19 N4 ? ? A G 12 A C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 13 A C 18 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog26 hydrog ? ? A G 22 N1 ? ? ? 1_555 A U 50 O2 ? ? A G 22 A U 50 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog27 hydrog ? ? A G 22 O6 ? ? ? 1_555 A U 50 N3 ? ? A G 22 A U 50 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog28 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 49 N3 ? ? A G 23 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 49 O2 ? ? A G 23 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 49 N4 ? ? A G 23 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 48 N1 ? ? A C 24 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 48 O6 ? ? A C 24 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 48 N2 ? ? A C 24 A G 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 27 N3 ? ? ? 1_555 A G 46 N1 ? ? A C 27 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 27 N4 ? ? ? 1_555 A G 46 O6 ? ? A C 27 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 27 O2 ? ? ? 1_555 A G 46 N2 ? ? A C 27 A G 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 28 N3 ? ? ? 1_555 A G 45 N1 ? ? A C 28 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 28 N4 ? ? ? 1_555 A G 45 O6 ? ? A C 28 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 28 O2 ? ? ? 1_555 A G 45 N2 ? ? A C 28 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A U 29 N3 ? ? ? 1_555 A A 44 N1 ? ? A U 29 A A 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A U 29 O4 ? ? ? 1_555 A A 44 N6 ? ? A U 29 A A 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 30 N1 ? ? ? 1_555 A C 42 N3 ? ? A G 30 A C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 30 N2 ? ? ? 1_555 A C 42 O2 ? ? A G 30 A C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 30 O6 ? ? ? 1_555 A C 42 N4 ? ? A G 30 A C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 41 N3 ? ? A G 31 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 41 O2 ? ? A G 31 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 41 N4 ? ? A G 31 A C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 31 N2 ? ? ? 1_555 A A 90 N3 ? ? A G 31 A A 90 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog49 hydrog ? ? A G 32 N1 ? ? ? 1_555 A C 40 N3 ? ? A G 32 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 32 N2 ? ? ? 1_555 A C 40 O2 ? ? A G 32 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A G 32 O6 ? ? ? 1_555 A C 40 N4 ? ? A G 32 A C 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 34 N4 ? ? ? 1_555 A G 96 O6 ? ? A C 34 A G 96 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog53 hydrog ? ? A G 35 N1 ? ? ? 1_555 A C 95 N3 ? ? A G 35 A C 95 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 35 N2 ? ? ? 1_555 A C 95 O2 ? ? A G 35 A C 95 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 35 O6 ? ? ? 1_555 A C 95 N4 ? ? A G 35 A C 95 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A G 36 N1 ? ? ? 1_555 A C 94 N3 ? ? A G 36 A C 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 36 N2 ? ? ? 1_555 A C 94 O2 ? ? A G 36 A C 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 36 O6 ? ? ? 1_555 A C 94 N4 ? ? A G 36 A C 94 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A A 37 N1 ? ? ? 1_555 A U 93 N3 ? ? A A 37 A U 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A A 37 N6 ? ? ? 1_555 A U 93 O4 ? ? A A 37 A U 93 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A C 38 N3 ? ? ? 1_555 A G 92 N1 ? ? A C 38 A G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A C 38 N4 ? ? ? 1_555 A G 92 O6 ? ? A C 38 A G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 38 O2 ? ? ? 1_555 A G 92 N2 ? ? A C 38 A G 92 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 42 O2 ? ? ? 1_555 A C 87 N4 ? ? A C 42 A C 87 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog65 hydrog ? ? A A 43 N3 ? ? ? 1_555 A A 44 N6 ? ? A A 43 A A 44 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog66 hydrog ? ? A G 45 N2 ? ? ? 1_555 A G 72 N3 ? ? A G 45 A G 72 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog67 hydrog ? ? A C 53 N3 ? ? ? 1_555 A G 66 N1 ? ? A C 53 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 53 N4 ? ? ? 1_555 A G 66 O6 ? ? A C 53 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A C 53 O2 ? ? ? 1_555 A G 66 N2 ? ? A C 53 A G 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A A 54 N1 ? ? ? 1_555 A U 65 N3 ? ? A A 54 A U 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A A 54 N6 ? ? ? 1_555 A U 65 O4 ? ? A A 54 A U 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A C 55 N3 ? ? ? 1_555 A G 64 N1 ? ? A C 55 A G 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog73 hydrog ? ? A C 55 N4 ? ? ? 1_555 A G 64 O6 ? ? A C 55 A G 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A C 55 O2 ? ? ? 1_555 A G 64 N2 ? ? A C 55 A G 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A C 56 N3 ? ? ? 1_555 A G 63 N1 ? ? A C 56 A G 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A C 56 N4 ? ? ? 1_555 A G 63 O6 ? ? A C 56 A G 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog77 hydrog ? ? A C 56 O2 ? ? ? 1_555 A G 63 N2 ? ? A C 56 A G 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A G 57 N1 ? ? ? 1_555 A C 62 N3 ? ? A G 57 A C 62 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? A G 57 N2 ? ? ? 1_555 A C 62 O2 ? ? A G 57 A C 62 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? A G 57 O6 ? ? ? 1_555 A C 62 N4 ? ? A G 57 A C 62 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? A G 72 N1 ? ? ? 1_555 A A 85 N1 ? ? A G 72 A A 85 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog82 hydrog ? ? A G 72 O6 ? ? ? 1_555 A A 85 N6 ? ? A G 72 A A 85 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog83 hydrog ? ? A G 73 N1 ? ? ? 1_555 A C 84 N3 ? ? A G 73 A C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? A G 73 N2 ? ? ? 1_555 A C 84 O2 ? ? A G 73 A C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? A G 73 O6 ? ? ? 1_555 A C 84 N4 ? ? A G 73 A C 84 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? A C 74 N3 ? ? ? 1_555 A G 83 N1 ? ? A C 74 A G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? A C 74 N4 ? ? ? 1_555 A G 83 O6 ? ? A C 74 A G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? A C 74 O2 ? ? ? 1_555 A G 83 N2 ? ? A C 74 A G 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? A C 75 N3 ? ? ? 1_555 A G 82 N1 ? ? A C 75 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? A C 75 N4 ? ? ? 1_555 A G 82 O6 ? ? A C 75 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog91 hydrog ? ? A C 75 O2 ? ? ? 1_555 A G 82 N2 ? ? A C 75 A G 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog92 hydrog ? ? A C 76 N3 ? ? ? 1_555 A G 81 N1 ? ? A C 76 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog93 hydrog ? ? A C 76 N4 ? ? ? 1_555 A G 81 O6 ? ? A C 76 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog94 hydrog ? ? A C 76 O2 ? ? ? 1_555 A G 81 N2 ? ? A C 76 A G 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog95 hydrog ? ? A G 77 N2 ? ? ? 1_555 A A 80 N7 ? ? A G 77 A A 80 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SAM 101 ? 13 'BINDING SITE FOR RESIDUE SAM A 101' AC2 Software A MG 105 ? 1 'BINDING SITE FOR RESIDUE MG A 105' AC3 Software A MG 106 ? 2 'BINDING SITE FOR RESIDUE MG A 106' # 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 13 A A 3 ? A A 3 . ? 1_555 ? 2 AC1 13 U A 4 ? U A 4 . ? 1_555 ? 3 AC1 13 C A 5 ? C A 5 . ? 1_555 ? 4 AC1 13 G A 8 ? G A 8 . ? 1_555 ? 5 AC1 13 A A 25 ? A A 25 . ? 1_555 ? 6 AC1 13 A A 26 ? A A 26 . ? 1_555 ? 7 AC1 13 C A 27 ? C A 27 . ? 1_555 ? 8 AC1 13 U A 47 ? U A 47 . ? 1_555 ? 9 AC1 13 G A 48 ? G A 48 . ? 1_555 ? 10 AC1 13 C A 49 ? C A 49 . ? 1_555 ? 11 AC1 13 A A 68 ? A A 68 . ? 1_555 ? 12 AC1 13 U A 69 ? U A 69 . ? 1_555 ? 13 AC1 13 C A 70 ? C A 70 . ? 1_555 ? 14 AC2 1 G A 58 ? G A 58 . ? 1_555 ? 15 AC3 2 A A 33 ? A A 33 . ? 1_555 ? 16 AC3 2 G A 36 ? G A 36 . ? 1_555 ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 P _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 G _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 OP3 _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 1 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.499 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation -0.108 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag 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 "O5'" A G 1 ? ? P A G 1 ? ? OP1 A G 1 ? ? 94.26 105.70 -11.44 0.90 N 2 1 "O5'" A G 1 ? ? P A G 1 ? ? OP2 A G 1 ? ? 118.03 110.70 7.33 1.20 N 3 1 C8 A A 3 ? ? N9 A A 3 ? ? C4 A A 3 ? ? 108.21 105.80 2.41 0.40 N 4 1 "O3'" A A 33 ? ? P A C 34 ? ? OP2 A C 34 ? ? 118.72 110.50 8.22 1.10 Y 5 1 C5 A U 69 ? ? C6 A U 69 ? ? N1 A U 69 ? ? 119.56 122.70 -3.14 0.50 N 6 1 C6 A C 70 ? ? N1 A C 70 ? ? C2 A C 70 ? ? 122.87 120.30 2.57 0.40 N 7 1 C5 A C 70 ? ? C6 A C 70 ? ? N1 A C 70 ? ? 117.64 121.00 -3.36 0.50 N 8 1 N1 A C 71 ? ? C2 A C 71 ? ? O2 A C 71 ? ? 115.22 118.90 -3.68 0.60 N # 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 MG MG MG N N 111 SAM N N N N 112 SAM CA C N S 113 SAM C C N N 114 SAM O O N N 115 SAM OXT O N N 116 SAM CB C N N 117 SAM CG C N N 118 SAM SD S N S 119 SAM CE C N N 120 SAM "C5'" C N N 121 SAM "C4'" C N S 122 SAM "O4'" O N N 123 SAM "C3'" C N S 124 SAM "O3'" O N N 125 SAM "C2'" C N R 126 SAM "O2'" O N N 127 SAM "C1'" C N R 128 SAM N9 N Y N 129 SAM C8 C Y N 130 SAM N7 N Y N 131 SAM C5 C Y N 132 SAM C6 C Y N 133 SAM N6 N N N 134 SAM N1 N Y N 135 SAM C2 C Y N 136 SAM N3 N Y N 137 SAM C4 C Y N 138 SAM HN1 H N N 139 SAM HN2 H N N 140 SAM HA H N N 141 SAM HB1 H N N 142 SAM HB2 H N N 143 SAM HG1 H N N 144 SAM HG2 H N N 145 SAM HE1 H N N 146 SAM HE2 H N N 147 SAM HE3 H N N 148 SAM "H5'1" H N N 149 SAM "H5'2" H N N 150 SAM "H4'" H N N 151 SAM "H3'" H N N 152 SAM "HO3'" H N N 153 SAM "H2'" H N N 154 SAM "HO2'" H N N 155 SAM "H1'" H N N 156 SAM H8 H N N 157 SAM HN61 H N N 158 SAM HN62 H N N 159 SAM H2 H N N 160 U OP3 O N N 161 U P P N N 162 U OP1 O N N 163 U OP2 O N N 164 U "O5'" O N N 165 U "C5'" C N N 166 U "C4'" C N R 167 U "O4'" O N N 168 U "C3'" C N S 169 U "O3'" O N N 170 U "C2'" C N R 171 U "O2'" O N N 172 U "C1'" C N R 173 U N1 N N N 174 U C2 C N N 175 U O2 O N N 176 U N3 N N N 177 U C4 C N N 178 U O4 O N N 179 U C5 C N N 180 U C6 C N N 181 U HOP3 H N N 182 U HOP2 H N N 183 U "H5'" H N N 184 U "H5''" H N N 185 U "H4'" H N N 186 U "H3'" H N N 187 U "HO3'" H N N 188 U "H2'" H N N 189 U "HO2'" H N N 190 U "H1'" H N N 191 U H3 H N N 192 U H5 H N N 193 U H6 H N N 194 # 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 SAM N CA sing N N 116 SAM N HN1 sing N N 117 SAM N HN2 sing N N 118 SAM CA C sing N N 119 SAM CA CB sing N N 120 SAM CA HA sing N N 121 SAM C O doub N N 122 SAM C OXT sing N N 123 SAM CB CG sing N N 124 SAM CB HB1 sing N N 125 SAM CB HB2 sing N N 126 SAM CG SD sing N N 127 SAM CG HG1 sing N N 128 SAM CG HG2 sing N N 129 SAM SD CE sing N N 130 SAM SD "C5'" sing N N 131 SAM CE HE1 sing N N 132 SAM CE HE2 sing N N 133 SAM CE HE3 sing N N 134 SAM "C5'" "C4'" sing N N 135 SAM "C5'" "H5'1" sing N N 136 SAM "C5'" "H5'2" sing N N 137 SAM "C4'" "O4'" sing N N 138 SAM "C4'" "C3'" sing N N 139 SAM "C4'" "H4'" sing N N 140 SAM "O4'" "C1'" sing N N 141 SAM "C3'" "O3'" sing N N 142 SAM "C3'" "C2'" sing N N 143 SAM "C3'" "H3'" sing N N 144 SAM "O3'" "HO3'" sing N N 145 SAM "C2'" "O2'" sing N N 146 SAM "C2'" "C1'" sing N N 147 SAM "C2'" "H2'" sing N N 148 SAM "O2'" "HO2'" sing N N 149 SAM "C1'" N9 sing N N 150 SAM "C1'" "H1'" sing N N 151 SAM N9 C8 sing Y N 152 SAM N9 C4 sing Y N 153 SAM C8 N7 doub Y N 154 SAM C8 H8 sing N N 155 SAM N7 C5 sing Y N 156 SAM C5 C6 sing Y N 157 SAM C5 C4 doub Y N 158 SAM C6 N6 sing N N 159 SAM C6 N1 doub Y N 160 SAM N6 HN61 sing N N 161 SAM N6 HN62 sing N N 162 SAM N1 C2 sing Y N 163 SAM C2 N3 doub Y N 164 SAM C2 H2 sing N N 165 SAM N3 C4 sing Y N 166 U OP3 P sing N N 167 U OP3 HOP3 sing N N 168 U P OP1 doub N N 169 U P OP2 sing N N 170 U P "O5'" sing N N 171 U OP2 HOP2 sing N N 172 U "O5'" "C5'" sing N N 173 U "C5'" "C4'" sing N N 174 U "C5'" "H5'" sing N N 175 U "C5'" "H5''" sing N N 176 U "C4'" "O4'" sing N N 177 U "C4'" "C3'" sing N N 178 U "C4'" "H4'" sing N N 179 U "O4'" "C1'" sing N N 180 U "C3'" "O3'" sing N N 181 U "C3'" "C2'" sing N N 182 U "C3'" "H3'" sing N N 183 U "O3'" "HO3'" sing N N 184 U "C2'" "O2'" sing N N 185 U "C2'" "C1'" sing N N 186 U "C2'" "H2'" sing N N 187 U "O2'" "HO2'" sing N N 188 U "C1'" N1 sing N N 189 U "C1'" "H1'" sing N N 190 U N1 C2 sing N N 191 U N1 C6 sing N N 192 U C2 O2 doub N N 193 U C2 N3 sing N N 194 U N3 C4 sing N N 195 U N3 H3 sing N N 196 U C4 O4 doub N N 197 U C4 C5 sing N N 198 U C5 C6 doub N N 199 U C5 H5 sing N N 200 U C6 H6 sing N N 201 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4OQU 'double helix' 4OQU 'a-form double helix' 4OQU 'hairpin loop' 4OQU tetraloop 4OQU 'bulge loop' 4OQU 'mismatched base pair' 4OQU 'triple helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 71 1_555 -1.486 -0.407 0.476 -3.858 -6.643 -1.465 1 A_G1:C71_A A 1 ? A 71 ? 19 1 1 A G 2 1_555 A C 70 1_555 -0.426 -0.248 0.195 -0.868 -9.313 -1.738 2 A_G2:C70_A A 2 ? A 70 ? 19 1 1 A A 3 1_555 A U 69 1_555 0.215 -0.230 0.405 6.763 -9.880 -3.545 3 A_A3:U69_A A 3 ? A 69 ? 20 1 1 A U 4 1_555 A A 68 1_555 0.138 -0.092 0.409 -7.892 -13.744 5.310 4 A_U4:A68_A A 4 ? A 68 ? 20 1 1 A C 5 1_555 A G 67 1_555 0.401 -0.224 0.467 -2.967 -5.013 -2.453 5 A_C5:G67_A A 5 ? A 67 ? 19 1 1 A C 53 1_555 A G 66 1_555 0.807 -0.590 -0.187 1.989 -12.168 -3.607 6 A_C53:G66_A A 53 ? A 66 ? 19 1 1 A A 54 1_555 A U 65 1_555 -0.706 -0.313 0.290 -2.005 -14.143 -5.513 7 A_A54:U65_A A 54 ? A 65 ? 20 1 1 A C 55 1_555 A G 64 1_555 -0.145 -0.035 0.247 4.782 -20.333 2.430 8 A_C55:G64_A A 55 ? A 64 ? 19 1 1 A C 56 1_555 A G 63 1_555 -0.371 -0.110 0.180 3.764 -11.873 -5.974 9 A_C56:G63_A A 56 ? A 63 ? 19 1 1 A G 57 1_555 A C 62 1_555 0.157 0.032 0.043 6.003 0.969 3.212 10 A_G57:C62_A A 57 ? A 62 ? 19 1 1 A C 18 1_555 A G 13 1_555 -0.109 0.771 -0.017 5.791 -0.209 7.369 11 A_C18:G13_A A 18 ? A 13 ? ? ? 1 A C 19 1_555 A G 12 1_555 -0.441 0.208 0.110 2.840 -1.678 4.255 12 A_C19:G12_A A 19 ? A 12 ? 19 1 1 A C 20 1_555 A G 11 1_555 1.077 -0.312 -0.078 -0.266 -3.413 -8.478 13 A_C20:G11_A A 20 ? A 11 ? 19 1 1 A C 21 1_555 A G 10 1_555 -0.523 0.120 0.159 -5.581 1.138 -4.923 14 A_C21:G10_A A 21 ? A 10 ? 19 1 1 A G 22 1_555 A U 50 1_555 -3.025 -0.592 0.016 2.789 -11.738 4.086 15 A_G22:U50_A A 22 ? A 50 ? 28 1 1 A G 23 1_555 A C 49 1_555 0.116 -0.078 0.117 -10.271 -17.683 -0.578 16 A_G23:C49_A A 23 ? A 49 ? 19 1 1 A C 24 1_555 A G 48 1_555 -0.069 -0.190 0.503 -18.394 -14.642 -6.159 17 A_C24:G48_A A 24 ? A 48 ? 19 1 1 A C 27 1_555 A G 46 1_555 -0.476 -0.323 -0.626 13.616 -6.785 -4.585 18 A_C27:G46_A A 27 ? A 46 ? 19 1 1 A C 28 1_555 A G 45 1_555 0.127 -0.360 -0.290 6.843 -3.709 2.381 19 A_C28:G45_A A 28 ? A 45 ? 19 1 1 A U 29 1_555 A A 44 1_555 0.433 -0.321 -0.284 -6.119 -7.561 -0.123 20 A_U29:A44_A A 29 ? A 44 ? 20 1 1 A G 30 1_555 A C 42 1_555 0.554 -0.180 0.367 7.465 -8.999 -5.268 21 A_G30:C42_A A 30 ? A 42 ? 19 1 1 A G 31 1_555 A C 41 1_555 0.371 -0.156 0.166 8.096 -10.052 1.290 22 A_G31:C41_A A 31 ? A 41 ? 19 1 1 A G 32 1_555 A C 40 1_555 -0.821 -0.325 -0.088 -0.455 -4.423 3.184 23 A_G32:C40_A A 32 ? A 40 ? 19 1 1 A G 92 1_555 A C 38 1_555 0.389 -0.129 0.422 2.061 -4.643 0.287 24 A_G92:C38_A A 92 ? A 38 ? 19 1 1 A U 93 1_555 A A 37 1_555 0.121 -0.192 0.270 0.041 -9.018 0.455 25 A_U93:A37_A A 93 ? A 37 ? 20 1 1 A C 94 1_555 A G 36 1_555 -0.273 0.216 -0.449 9.002 -9.297 6.693 26 A_C94:G36_A A 94 ? A 36 ? 19 1 1 A C 95 1_555 A G 35 1_555 0.231 0.089 -0.022 6.438 -11.392 3.564 27 A_C95:G35_A A 95 ? A 35 ? 19 1 1 A G 96 1_555 A C 34 1_555 0.374 0.414 -0.376 -14.552 -13.763 -4.260 28 A_G96:C34_A A 96 ? A 34 ? ? 1 1 A G 72 1_555 A A 85 1_555 -0.157 1.514 -0.110 0.054 8.737 -18.831 29 A_G72:A85_A A 72 ? A 85 ? 8 1 1 A G 73 1_555 A C 84 1_555 0.605 0.120 -0.145 3.887 -5.015 1.405 30 A_G73:C84_A A 73 ? A 84 ? 19 1 1 A C 74 1_555 A G 83 1_555 -0.146 -0.055 -0.906 20.448 -14.115 3.496 31 A_C74:G83_A A 74 ? A 83 ? 19 1 1 A C 75 1_555 A G 82 1_555 0.188 -0.166 -0.982 16.389 -12.089 3.422 32 A_C75:G82_A A 75 ? A 82 ? 19 1 1 A C 76 1_555 A G 81 1_555 -0.182 0.085 -0.339 4.751 -4.854 4.958 33 A_C76:G81_A A 76 ? A 81 ? 19 1 1 A G 77 1_555 A A 80 1_555 7.887 -5.527 0.551 11.400 7.161 -38.844 34 A_G77:A80_A A 77 ? A 80 ? ? ? # 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 1 1_555 A C 71 1_555 A G 2 1_555 A C 70 1_555 -0.562 -1.423 3.187 1.982 4.654 38.111 -2.708 1.086 2.968 7.089 -3.019 38.433 1 AA_G1G2:C70C71_AA A 1 ? A 71 ? A 2 ? A 70 ? 1 A G 2 1_555 A C 70 1_555 A A 3 1_555 A U 69 1_555 0.375 -1.433 3.094 -0.017 5.815 33.027 -3.353 -0.652 2.808 10.131 0.029 33.522 2 AA_G2A3:U69C70_AA A 2 ? A 70 ? A 3 ? A 69 ? 1 A A 3 1_555 A U 69 1_555 A U 4 1_555 A A 68 1_555 0.932 -1.675 3.631 4.331 17.185 33.906 -4.770 -0.871 2.611 27.280 -6.875 38.137 3 AA_A3U4:A68U69_AA A 3 ? A 69 ? A 4 ? A 68 ? 1 A U 4 1_555 A A 68 1_555 A C 5 1_555 A G 67 1_555 0.148 -2.004 3.085 2.292 4.476 30.298 -4.577 0.127 2.770 8.490 -4.348 30.703 4 AA_U4C5:G67A68_AA A 4 ? A 68 ? A 5 ? A 67 ? 1 A C 5 1_555 A G 67 1_555 A C 53 1_555 A G 66 1_555 -2.042 -1.437 3.072 4.710 -0.980 49.840 -1.633 2.725 2.906 -1.160 -5.574 50.057 5 AA_C5C53:G66G67_AA A 5 ? A 67 ? A 53 ? A 66 ? 1 A C 53 1_555 A G 66 1_555 A A 54 1_555 A U 65 1_555 -0.483 -1.759 3.121 -3.322 14.973 22.719 -6.729 0.354 1.707 33.541 7.441 27.355 6 AA_C53A54:U65G66_AA A 53 ? A 66 ? A 54 ? A 65 ? 1 A A 54 1_555 A U 65 1_555 A C 55 1_555 A G 64 1_555 0.098 -1.347 3.114 1.112 1.299 34.912 -2.427 -0.004 3.065 2.163 -1.852 34.953 7 AA_A54C55:G64U65_AA A 54 ? A 65 ? A 55 ? A 64 ? 1 A C 55 1_555 A G 64 1_555 A C 56 1_555 A G 63 1_555 0.040 -1.490 3.222 0.506 5.925 35.215 -3.243 0.004 2.941 9.707 -0.829 35.698 8 AA_C55C56:G63G64_AA A 55 ? A 64 ? A 56 ? A 63 ? 1 A C 56 1_555 A G 63 1_555 A G 57 1_555 A C 62 1_555 0.823 -1.648 3.224 3.300 7.524 33.688 -3.860 -0.903 2.866 12.748 -5.591 34.647 9 AA_C56G57:C62G63_AA A 56 ? A 63 ? A 57 ? A 62 ? 1 A C 18 1_555 A G 13 1_555 A C 19 1_555 A G 12 1_555 -0.069 -1.909 3.249 -3.891 7.882 28.890 -5.144 -0.596 2.635 15.356 7.579 30.171 10 AA_C18C19:G12G13_AA A 18 ? A 13 ? A 19 ? A 12 ? 1 A C 19 1_555 A G 12 1_555 A C 20 1_555 A G 11 1_555 -1.140 -1.612 3.356 2.866 6.052 41.325 -2.879 1.890 3.019 8.508 -4.029 41.840 11 AA_C19C20:G11G12_AA A 19 ? A 12 ? A 20 ? A 11 ? 1 A C 20 1_555 A G 11 1_555 A C 21 1_555 A G 10 1_555 0.421 -1.552 3.235 2.019 11.917 23.820 -6.123 -0.444 2.242 26.776 -4.535 26.672 12 AA_C20C21:G10G11_AA A 20 ? A 11 ? A 21 ? A 10 ? 1 A C 21 1_555 A G 10 1_555 A G 22 1_555 A U 50 1_555 2.086 -1.229 2.879 -2.251 10.271 26.035 -4.441 -4.723 2.070 21.705 4.757 28.044 13 AA_C21G22:U50G10_AA A 21 ? A 10 ? A 22 ? A 50 ? 1 A G 22 1_555 A U 50 1_555 A G 23 1_555 A C 49 1_555 -0.182 -1.643 3.670 -5.108 3.312 46.706 -2.358 -0.237 3.552 4.157 6.411 47.079 14 AA_G22G23:C49U50_AA A 22 ? A 50 ? A 23 ? A 49 ? 1 A G 23 1_555 A C 49 1_555 A C 24 1_555 A G 48 1_555 -0.701 -1.469 3.218 -3.092 1.778 36.574 -2.569 0.697 3.192 2.825 4.913 36.742 15 AA_G23C24:G48C49_AA A 23 ? A 49 ? A 24 ? A 48 ? 1 A C 27 1_555 A G 46 1_555 A C 28 1_555 A G 45 1_555 -0.242 -2.278 3.472 -3.717 7.500 33.108 -5.061 -0.173 2.910 12.907 6.396 34.121 16 AA_C27C28:G45G46_AA A 27 ? A 46 ? A 28 ? A 45 ? 1 A C 28 1_555 A G 45 1_555 A U 29 1_555 A A 44 1_555 0.458 -2.075 3.474 4.483 6.142 36.984 -4.020 -0.117 3.134 9.558 -6.977 37.730 17 AA_C28U29:A44G45_AA A 28 ? A 45 ? A 29 ? A 44 ? 1 A U 29 1_555 A A 44 1_555 A G 30 1_555 A C 42 1_555 2.018 -1.475 3.223 -12.852 7.499 49.754 -2.136 -3.076 2.435 8.692 14.895 51.795 18 AA_U29G30:C42A44_AA A 29 ? A 44 ? A 30 ? A 42 ? 1 A G 30 1_555 A C 42 1_555 A G 31 1_555 A C 41 1_555 0.072 -1.601 3.299 0.364 5.460 33.737 -3.564 -0.067 3.011 9.331 -0.621 34.165 19 AA_G30G31:C41C42_AA A 30 ? A 42 ? A 31 ? A 41 ? 1 A G 31 1_555 A C 41 1_555 A G 32 1_555 A C 40 1_555 1.036 -2.501 3.327 3.186 5.020 21.973 -8.064 -1.532 2.813 12.870 -8.168 22.753 20 AA_G31G32:C40C41_AA A 31 ? A 41 ? A 32 ? A 40 ? 1 A G 32 1_555 A C 40 1_555 A G 92 1_555 A C 38 1_555 -1.145 0.723 3.411 -5.571 -4.282 86.978 0.621 0.703 3.434 -3.107 4.042 87.205 21 AA_G32G92:C38C40_AA A 32 ? A 40 ? A 92 ? A 38 ? 1 A G 92 1_555 A C 38 1_555 A U 93 1_555 A A 37 1_555 -0.405 -1.607 3.370 -1.275 7.431 31.281 -4.201 0.509 2.934 13.536 2.322 32.155 22 AA_G92U93:A37C38_AA A 92 ? A 38 ? A 93 ? A 37 ? 1 A U 93 1_555 A A 37 1_555 A C 94 1_555 A G 36 1_555 0.173 -1.413 2.903 6.237 10.730 27.961 -4.427 0.685 2.211 20.950 -12.177 30.541 23 AA_U93C94:G36A37_AA A 93 ? A 37 ? A 94 ? A 36 ? 1 A C 94 1_555 A G 36 1_555 A C 95 1_555 A G 35 1_555 0.043 -1.341 3.306 -3.415 13.057 32.550 -4.044 -0.549 2.579 22.146 5.792 35.167 24 AA_C94C95:G35G36_AA A 94 ? A 36 ? A 95 ? A 35 ? 1 A C 95 1_555 A G 35 1_555 A G 96 1_555 A C 34 1_555 0.053 -2.041 3.850 2.902 12.044 32.838 -5.333 0.381 2.937 20.421 -4.921 35.037 25 AA_C95G96:C34G35_AA A 95 ? A 35 ? A 96 ? A 34 ? 1 A G 72 1_555 A A 85 1_555 A G 73 1_555 A C 84 1_555 0.911 -1.817 3.202 -1.756 8.793 34.235 -4.166 -1.734 2.621 14.628 2.922 35.356 26 AA_G72G73:C84A85_AA A 72 ? A 85 ? A 73 ? A 84 ? 1 A G 73 1_555 A C 84 1_555 A C 74 1_555 A G 83 1_555 0.695 -1.405 2.948 4.985 0.272 29.444 -2.779 -0.398 3.010 0.530 -9.720 29.855 27 AA_G73C74:G83C84_AA A 73 ? A 84 ? A 74 ? A 83 ? 1 A C 74 1_555 A G 83 1_555 A C 75 1_555 A G 82 1_555 -0.126 -1.436 3.677 1.807 6.616 32.604 -3.698 0.545 3.319 11.625 -3.175 33.298 28 AA_C74C75:G82G83_AA A 74 ? A 83 ? A 75 ? A 82 ? 1 A C 75 1_555 A G 82 1_555 A C 76 1_555 A G 81 1_555 0.244 -1.800 3.482 -2.554 14.751 28.525 -5.721 -0.868 2.271 27.661 4.789 32.143 29 AA_C75C76:G81G82_AA A 75 ? A 82 ? A 76 ? A 81 ? 1 A C 76 1_555 A G 81 1_555 A G 77 1_555 A A 80 1_555 -3.610 -2.026 3.007 -8.138 2.713 57.700 -2.220 3.288 3.355 2.794 8.381 58.280 30 AA_C76G77:A80G81_AA A 76 ? A 81 ? A 77 ? A 80 ? # _atom_sites.entry_id 4OQU _atom_sites.fract_transf_matrix[1][1] 0.007857 _atom_sites.fract_transf_matrix[1][2] 0.004536 _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] 0.009073 _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] 0.005506 _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 MG N O P S # loop_