data_1MSY # _entry.id 1MSY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1MSY pdb_00001msy 10.2210/pdb1msy/pdb NDB UR0026 ? ? RCSB RCSB017157 ? ? WWPDB D_1000017157 ? ? # 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 2003-02-25 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2024-02-14 # _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' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1MSY _pdbx_database_status.recvd_initial_deposition_date 2002-09-19 _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.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 480D 'WT Sarcin/Ricin domain from E. Coli 23 S rRNA' unspecified PDB 1JBR 'Ribotoxin Restrictocin and a 31- Mer SRD RNA inhibitor' unspecified PDB 1JBS 'Ribotoxin Restrictocin and a 29-Mer SRD RNA analog' unspecified PDB 1JBT 'Ribotoxin Restrictocin and a 29-Mer SRD RNA analog' unspecified PDB 483D 'WT Sarcin/Ricin domain from E. Coli 23 S rRNA' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Correll, C.C.' 1 'Swinger, K.' 2 # _citation.id primary _citation.title 'Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution' _citation.journal_abbrev RNA _citation.journal_volume 9 _citation.page_first 355 _citation.page_last 363 _citation.year 2003 _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 12592009 _citation.pdbx_database_id_DOI 10.1261/rna.2147803 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Correll, C.C.' 1 ? primary 'Swinger, K.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'SARCIN/RICIN DOMAIN FROM 23 S RRNA' 8705.215 1 ? 'A2660U, G2661A' ? 'GUAA tetraloop mutant' 2 water nat water 18.015 109 ? ? ? ? # _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 UGCUCCUAGUACGUAAGGACCGGAGUG _entity_poly.pdbx_seq_one_letter_code_can UGCUCCUAGUACGUAAGGACCGGAGUG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 G n 1 3 C n 1 4 U n 1 5 C n 1 6 C n 1 7 U n 1 8 A n 1 9 G n 1 10 U n 1 11 A n 1 12 C n 1 13 G n 1 14 U n 1 15 A n 1 16 A n 1 17 G n 1 18 G n 1 19 A n 1 20 C n 1 21 C n 1 22 G n 1 23 G n 1 24 A n 1 25 G n 1 26 U n 1 27 G 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 'A2660U and G2661U double mutant of the SRL domain from E.coli rRNA' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 U 1 2647 2647 U URI A . n A 1 2 G 2 2648 2648 G GUA A . n A 1 3 C 3 2649 2649 C CYT A . n A 1 4 U 4 2650 2650 U URI A . n A 1 5 C 5 2651 2651 C CYT A . n A 1 6 C 6 2652 2652 C CYT A . n A 1 7 U 7 2653 2653 U URI A . n A 1 8 A 8 2654 2654 A ADE A . n A 1 9 G 9 2655 2655 G GUA A . n A 1 10 U 10 2656 2656 U URI A . n A 1 11 A 11 2657 2657 A ADE A . n A 1 12 C 12 2658 2658 C CYT A . n A 1 13 G 13 2659 2659 G GUA A . n A 1 14 U 14 2660 2660 U URI A . n A 1 15 A 15 2661 2661 A ADE A . n A 1 16 A 16 2662 2662 A ADE A . n A 1 17 G 17 2663 2663 G GUA A . n A 1 18 G 18 2664 2664 G GUA A . n A 1 19 A 19 2665 2665 A ADE A . n A 1 20 C 20 2666 2666 C CYT A . n A 1 21 C 21 2667 2667 C CYT A . n A 1 22 G 22 2668 2668 G GUA A . n A 1 23 G 23 2669 2669 G GUA A . n A 1 24 A 24 2670 2670 A ADE A . n A 1 25 G 25 2671 2671 G GUA A . n A 1 26 U 26 2672 2672 U URI A . n A 1 27 G 27 2673 2673 G GUA 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 HOH 1 3001 3001 HOH HOH A . B 2 HOH 2 3002 3002 HOH HOH A . B 2 HOH 3 3003 3003 HOH HOH A . B 2 HOH 4 3004 3004 HOH HOH A . B 2 HOH 5 3005 3005 HOH HOH A . B 2 HOH 6 3006 3006 HOH HOH A . B 2 HOH 7 3007 3007 HOH HOH A . B 2 HOH 8 3008 3008 HOH HOH A . B 2 HOH 9 3009 3009 HOH HOH A . B 2 HOH 10 3010 3010 HOH HOH A . B 2 HOH 11 3011 3011 HOH HOH A . B 2 HOH 12 3012 3012 HOH HOH A . B 2 HOH 13 3013 3013 HOH HOH A . B 2 HOH 14 3014 3014 HOH HOH A . B 2 HOH 15 3015 3015 HOH HOH A . B 2 HOH 16 3016 3016 HOH HOH A . B 2 HOH 17 3017 3017 HOH HOH A . B 2 HOH 18 3018 3018 HOH HOH A . B 2 HOH 19 3019 3019 HOH HOH A . B 2 HOH 20 3020 3020 HOH HOH A . B 2 HOH 21 3021 3021 HOH HOH A . B 2 HOH 22 3022 3022 HOH HOH A . B 2 HOH 23 3023 3023 HOH HOH A . B 2 HOH 24 3024 3024 HOH HOH A . B 2 HOH 25 3025 3025 HOH HOH A . B 2 HOH 26 3026 3026 HOH HOH A . B 2 HOH 27 3027 3027 HOH HOH A . B 2 HOH 28 3028 3028 HOH HOH A . B 2 HOH 29 3029 3029 HOH HOH A . B 2 HOH 30 3030 3030 HOH HOH A . B 2 HOH 31 3031 3031 HOH HOH A . B 2 HOH 32 3032 3032 HOH HOH A . B 2 HOH 33 3033 3033 HOH HOH A . B 2 HOH 34 3034 3034 HOH HOH A . B 2 HOH 35 3035 3035 HOH HOH A . B 2 HOH 36 3036 3036 HOH HOH A . B 2 HOH 37 3037 3037 HOH HOH A . B 2 HOH 38 3038 3038 HOH HOH A . B 2 HOH 39 3039 3039 HOH HOH A . B 2 HOH 40 3040 3040 HOH HOH A . B 2 HOH 41 3041 3041 HOH HOH A . B 2 HOH 42 3042 3042 HOH HOH A . B 2 HOH 43 3043 3043 HOH HOH A . B 2 HOH 44 3044 3044 HOH HOH A . B 2 HOH 45 3045 3045 HOH HOH A . B 2 HOH 46 3046 3046 HOH HOH A . B 2 HOH 47 3047 3047 HOH HOH A . B 2 HOH 48 3048 3048 HOH HOH A . B 2 HOH 49 3049 3049 HOH HOH A . B 2 HOH 50 3050 3050 HOH HOH A . B 2 HOH 51 3051 3051 HOH HOH A . B 2 HOH 52 3052 3052 HOH HOH A . B 2 HOH 53 3053 3053 HOH HOH A . B 2 HOH 54 3054 3054 HOH HOH A . B 2 HOH 55 3055 3055 HOH HOH A . B 2 HOH 56 3056 3056 HOH HOH A . B 2 HOH 57 3057 3057 HOH HOH A . B 2 HOH 58 3058 3058 HOH HOH A . B 2 HOH 59 3059 3059 HOH HOH A . B 2 HOH 60 3060 3060 HOH HOH A . B 2 HOH 61 3061 3061 HOH HOH A . B 2 HOH 62 3062 3062 HOH HOH A . B 2 HOH 63 3063 3063 HOH HOH A . B 2 HOH 64 3064 3064 HOH HOH A . B 2 HOH 65 3065 3065 HOH HOH A . B 2 HOH 66 3066 3066 HOH HOH A . B 2 HOH 67 3067 3067 HOH HOH A . B 2 HOH 68 3068 3068 HOH HOH A . B 2 HOH 69 3069 3069 HOH HOH A . B 2 HOH 70 3070 3070 HOH HOH A . B 2 HOH 71 3071 3071 HOH HOH A . B 2 HOH 72 3072 3072 HOH HOH A . B 2 HOH 73 3073 3073 HOH HOH A . B 2 HOH 74 3074 3074 HOH HOH A . B 2 HOH 75 3075 3075 HOH HOH A . B 2 HOH 76 3076 3076 HOH HOH A . B 2 HOH 77 3077 3077 HOH HOH A . B 2 HOH 78 3078 3078 HOH HOH A . B 2 HOH 79 3079 3079 HOH HOH A . B 2 HOH 80 3080 3080 HOH HOH A . B 2 HOH 81 3081 3081 HOH HOH A . B 2 HOH 82 3082 3082 HOH HOH A . B 2 HOH 83 3083 3083 HOH HOH A . B 2 HOH 84 3084 3084 HOH HOH A . B 2 HOH 85 3086 3086 HOH HOH A . B 2 HOH 86 3087 3087 HOH HOH A . B 2 HOH 87 3088 3088 HOH HOH A . B 2 HOH 88 3089 3089 HOH HOH A . B 2 HOH 89 3090 3090 HOH HOH A . B 2 HOH 90 3091 3091 HOH HOH A . B 2 HOH 91 3092 3092 HOH HOH A . B 2 HOH 92 3093 3093 HOH HOH A . B 2 HOH 93 3094 3094 HOH HOH A . B 2 HOH 94 3095 3095 HOH HOH A . B 2 HOH 95 3096 3096 HOH HOH A . B 2 HOH 96 3098 3098 HOH HOH A . B 2 HOH 97 3099 3099 HOH HOH A . B 2 HOH 98 3100 3100 HOH HOH A . B 2 HOH 99 3101 3101 HOH HOH A . B 2 HOH 100 3102 3102 HOH HOH A . B 2 HOH 101 3103 3103 HOH HOH A . B 2 HOH 102 3104 3104 HOH HOH A . B 2 HOH 103 3105 3105 HOH HOH A . B 2 HOH 104 3107 3107 HOH HOH A . B 2 HOH 105 3108 3108 HOH HOH A . B 2 HOH 106 3109 3109 HOH HOH A . B 2 HOH 107 3110 3110 HOH HOH A . B 2 HOH 108 3111 3111 HOH HOH A . B 2 HOH 109 3112 3112 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 SCALEPACK 'data scaling' . ? 2 CNS refinement . ? 3 DENZO 'data reduction' . ? 4 CNS phasing . ? 5 # _cell.entry_id 1MSY _cell.length_a 57.974 _cell.length_b 22.534 _cell.length_c 58.465 _cell.angle_alpha 90.00 _cell.angle_beta 101.72 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MSY _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # _exptl.entry_id 1MSY _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.73 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 292 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'ammonium sulfate, potassium MOPS, magnesium chloride, manganese chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K' _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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 '(NH4)2SO4' ? ? ? 1 2 1 'potassium MOPS' ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 MnCl2 ? ? ? 1 5 2 '(NH4)2SO4' ? ? ? 1 6 2 MgCl2 ? ? ? 1 7 2 MnCl2 ? ? ? # _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 CUSTOM-MADE _diffrn_detector.pdbx_collection_date 2000-07-06 _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 'Si-111 double crystal monochromator' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97764 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97764 # _reflns.entry_id 1MSY _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 40.0 _reflns.d_resolution_high 1.40 _reflns.number_obs 14372 _reflns.number_all 14372 _reflns.percent_possible_obs 97.9 _reflns.pdbx_Rmerge_I_obs 0.072 _reflns.pdbx_Rsym_value 0.072 _reflns.pdbx_netI_over_sigmaI 21.8 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.3 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.40 _reflns_shell.d_res_low 1.42 _reflns_shell.percent_possible_all 80.0 _reflns_shell.Rmerge_I_obs 0.323 _reflns_shell.pdbx_Rsym_value 0.323 _reflns_shell.meanI_over_sigI_obs 2.3 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1MSY _refine.ls_number_reflns_obs 14372 _refine.ls_number_reflns_all 14372 _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.ls_d_res_low 29.0 _refine.ls_d_res_high 1.41 _refine.ls_percent_reflns_obs 97.9 _refine.ls_R_factor_obs 0.1637 _refine.ls_R_factor_all 0.1637 _refine.ls_R_factor_R_work 0.164 _refine.ls_R_factor_R_free 0.207 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 11.0 _refine.ls_number_reflns_R_free 1419 _refine.ls_number_parameters 6236 _refine.ls_number_restraints 8182 _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ;ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ? ; _refine.pdbx_starting_model 483D _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 RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1MSY _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 2 _refine_analyze.occupancy_sum_hydrogen 0.00 _refine_analyze.occupancy_sum_non_hydrogen 662.50 _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 582 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 109 _refine_hist.number_atoms_total 691 _refine_hist.d_res_high 1.41 _refine_hist.d_res_low 29.0 # 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 0.010 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.028 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0195 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.079 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1MSY _pdbx_refine.R_factor_all_no_cutoff 0.1637 _pdbx_refine.R_factor_obs_no_cutoff 0.164 _pdbx_refine.free_R_factor_no_cutoff 0.207 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 11.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1419 _pdbx_refine.R_factor_all_4sig_cutoff 0.1383 _pdbx_refine.R_factor_obs_4sig_cutoff 0.1366 _pdbx_refine.free_R_factor_4sig_cutoff 0.1784 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 10.8 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 1082 _pdbx_refine.number_reflns_obs_4sig_cutoff 10030 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1MSY _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 1MSY _struct.title 'GUAA tetraloop mutant of Sarcin/Ricin domain from E. Coli 23 S rRNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1MSY _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;A-minor motif, sarcin/ricin loop, RNA structure, RNA tertiary contacts, RNA motifs, conformational change, RNA-protein recognition, hydration, 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 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1MSY _struct_ref.pdbx_db_accession 1MSY _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1MSY _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 27 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1MSY _struct_ref_seq.db_align_beg 2647 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 2673 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2647 _struct_ref_seq.pdbx_auth_seq_align_end 2673 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 # _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.pdbx_parent_biol_id ? _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 U 1 O4 ? ? ? 1_555 A G 27 N1 ? ? A U 2647 A G 2673 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog2 hydrog ? ? A G 2 N1 ? ? ? 1_555 A U 26 O2 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 A U 26 N3 ? ? A G 2648 A U 2672 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 25 N1 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 25 O6 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 25 N2 ? ? A C 2649 A G 2671 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 4 N3 ? ? ? 1_555 A A 24 N1 ? ? A U 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A U 4 O4 ? ? ? 1_555 A A 24 N6 ? ? A U 2650 A A 2670 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 5 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 2651 A G 2669 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 22 N1 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 22 O6 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 2652 A G 2668 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 7 O2 ? ? ? 1_555 A C 21 N4 ? ? A U 2653 A C 2667 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog16 hydrog ? ? A G 9 N2 ? ? ? 1_555 A U 10 O4 ? ? A G 2655 A U 2656 1_555 ? ? ? ? ? ? 'G-U MISPAIR' ? ? ? hydrog17 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 19 N7 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog18 hydrog ? ? A U 10 O2 ? ? ? 1_555 A A 19 N6 ? ? A U 2656 A A 2665 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog19 hydrog ? ? A A 11 N6 ? ? ? 1_555 A G 18 N3 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A A 11 N7 ? ? ? 1_555 A G 18 N2 ? ? A A 2657 A G 2664 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog21 hydrog ? ? A C 12 N3 ? ? ? 1_555 A G 17 N1 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 N4 ? ? ? 1_555 A G 17 O6 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 O2 ? ? ? 1_555 A G 17 N2 ? ? A C 2658 A G 2663 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 13 N2 ? ? ? 1_555 A A 16 N7 ? ? A G 2659 A A 2662 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 N1 A A 2657 ? ? C2 A A 2657 ? ? N3 A A 2657 ? ? 132.68 129.30 3.38 0.50 N 2 1 N9 A G 2659 ? ? "C1'" A G 2659 ? ? "C2'" A G 2659 ? ? 103.31 112.00 -8.69 1.10 N 3 1 C2 A G 2659 ? ? N3 A G 2659 ? ? C4 A G 2659 ? ? 114.98 111.90 3.08 0.50 N 4 1 C5 A G 2659 ? ? C6 A G 2659 ? ? N1 A G 2659 ? ? 114.59 111.50 3.09 0.50 N 5 1 "C3'" A A 2662 ? ? "O3'" A A 2662 ? ? P A G 2663 ? A 111.28 119.70 -8.42 1.20 Y 6 1 "O5'" A G 2663 ? ? P A G 2663 ? B OP1 A G 2663 ? B 118.11 110.70 7.41 1.20 N 7 1 C5 A G 2664 ? ? C6 A G 2664 ? ? O6 A G 2664 ? ? 124.45 128.60 -4.15 0.60 N 8 1 N1 A G 2673 ? ? C6 A G 2673 ? ? O6 A G 2673 ? ? 115.57 119.90 -4.33 0.60 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 A U 2647 ? A U 1 2 1 A G 2673 ? A G 27 3 1 A HOH 3002 ? B HOH . 4 1 A HOH 3004 ? B HOH . 5 1 A HOH 3068 ? B HOH . # _pdbx_database_remark.id 400 _pdbx_database_remark.text ;COMPOUND A CRYSTALLOGRAPHIC TWO-FOLD AXIS PASSES THROUGH THE TERMINAL GU WOBBLEBASE PAIR. EACH MOLECULE ABOUT THE 2-FOLD CONTRIBUTES ONE NUCLEOTIDE TO THE WOBBLE PAIR AND THE NUCLEOTIDE THAT COULD FORM THE INTRAMOLECULAR CLOSING PAIR IS DISORDERED. NOTE THAT THE OCCUPANCIES FOR THESE NUCLEOTIDES IS 0.5. ; # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1MSY 'double helix' 1MSY 'a-form double helix' 1MSY 'mismatched base pair' 1MSY '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 U 1 1_555 A G 27 1_555 -1.590 0.316 -0.263 1.954 -3.602 -43.734 1 A_U2647:G2673_A A 2647 ? A 2673 ? ? ? 1 A G 2 1_555 A U 26 1_555 -2.367 -0.597 0.107 4.665 -7.747 -2.953 2 A_G2648:U2672_A A 2648 ? A 2672 ? 28 ? 1 A C 3 1_555 A G 25 1_555 0.087 -0.169 0.021 9.595 -15.927 -2.310 3 A_C2649:G2671_A A 2649 ? A 2671 ? 19 1 1 A U 4 1_555 A A 24 1_555 0.109 -0.111 0.249 4.923 -16.454 6.329 4 A_U2650:A2670_A A 2650 ? A 2670 ? 20 1 1 A C 5 1_555 A G 23 1_555 0.186 -0.103 -0.072 1.460 -17.745 3.271 5 A_C2651:G2669_A A 2651 ? A 2669 ? 19 1 1 A C 6 1_555 A G 22 1_555 0.285 -0.107 0.257 -4.322 -8.628 0.533 6 A_C2652:G2668_A A 2652 ? A 2668 ? 19 1 1 A U 7 1_555 A C 21 1_555 5.745 -2.187 -0.252 -0.399 -12.063 -15.307 7 A_U2653:C2667_A A 2653 ? A 2667 ? ? ? 1 A U 10 1_555 A A 19 1_555 4.035 -1.616 -0.496 8.420 -17.415 -106.047 8 A_U2656:A2665_A A 2656 ? A 2665 ? 24 4 1 A A 11 1_555 A G 18 1_555 -6.873 -4.208 -0.064 -1.133 2.564 -0.455 9 A_A2657:G2664_A A 2657 ? A 2664 ? 11 9 1 A C 12 1_555 A G 17 1_555 0.121 -0.106 -0.289 6.738 -3.956 1.141 10 A_C2658:G2663_A A 2658 ? A 2663 ? 19 1 1 A G 13 1_555 A A 16 1_555 6.786 -4.822 1.187 -0.984 -18.469 -11.757 11 A_G2659:A2662_A A 2659 ? A 2662 ? ? 10 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A U 1 1_555 A G 27 1_555 A G 2 1_555 A U 26 1_555 2.964 -1.315 3.218 -5.289 6.766 34.803 -2.995 -5.490 2.465 11.104 8.680 35.815 1 AA_U2647G2648:U2672G2673_AA A 2647 ? A 2673 ? A 2648 ? A 2672 ? 1 A G 2 1_555 A U 26 1_555 A C 3 1_555 A G 25 1_555 -0.235 -1.261 3.127 -2.093 3.784 41.783 -2.129 0.123 3.014 5.288 2.925 41.997 2 AA_G2648C2649:G2671U2672_AA A 2648 ? A 2672 ? A 2649 ? A 2671 ? 1 A C 3 1_555 A G 25 1_555 A U 4 1_555 A A 24 1_555 0.788 -1.420 3.246 -0.330 7.258 33.482 -3.494 -1.388 2.877 12.418 0.565 34.239 3 AA_C2649U2650:A2670G2671_AA A 2649 ? A 2671 ? A 2650 ? A 2670 ? 1 A U 4 1_555 A A 24 1_555 A C 5 1_555 A G 23 1_555 -0.448 -1.599 3.232 2.117 3.948 33.526 -3.358 1.097 2.997 6.807 -3.649 33.816 4 AA_U2650C2651:G2669A2670_AA A 2650 ? A 2670 ? A 2651 ? A 2669 ? 1 A C 5 1_555 A G 23 1_555 A C 6 1_555 A G 22 1_555 -0.133 -1.725 3.372 -1.242 8.010 29.668 -4.771 0.016 2.823 15.287 2.371 30.731 5 AA_C2651C2652:G2668G2669_AA A 2651 ? A 2669 ? A 2652 ? A 2668 ? 1 A C 6 1_555 A G 22 1_555 A U 7 1_555 A C 21 1_555 -1.098 -1.100 3.362 6.243 4.203 52.001 -1.518 1.648 3.129 4.765 -7.078 52.506 6 AA_C2652U2653:C2667G2668_AA A 2652 ? A 2668 ? A 2653 ? A 2667 ? 1 A U 7 1_555 A C 21 1_555 A U 10 1_555 A A 19 1_555 0.497 -0.569 6.407 4.388 -4.755 30.954 0.703 0.699 6.429 -8.790 -8.111 31.607 7 AA_U2653U2656:A2665C2667_AA A 2653 ? A 2667 ? A 2656 ? A 2665 ? 1 A U 10 1_555 A A 19 1_555 A A 11 1_555 A G 18 1_555 5.495 -1.210 3.557 -1.906 -3.677 -13.990 8.486 19.712 3.823 14.680 -7.611 -14.587 8 AA_U2656A2657:G2664A2665_AA A 2656 ? A 2665 ? A 2657 ? A 2664 ? 1 A A 11 1_555 A G 18 1_555 A C 12 1_555 A G 17 1_555 -0.284 -0.971 3.217 -1.816 4.959 60.478 -1.195 0.195 3.143 4.913 1.799 60.686 9 AA_A2657C2658:G2663G2664_AA A 2657 ? A 2664 ? A 2658 ? A 2663 ? 1 A C 12 1_555 A G 17 1_555 A G 13 1_555 A A 16 1_555 -3.036 -1.156 3.386 -3.711 15.028 43.049 -2.834 3.583 3.076 19.734 4.873 45.623 10 AA_C2658G2659:A2662G2663_AA A 2658 ? A 2663 ? A 2659 ? A 2662 ? # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 483D _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 1MSY _atom_sites.fract_transf_matrix[1][1] 0.017249 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.003578 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.044377 _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] 0.017468 _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 # loop_