data_1S34 # _entry.id 1S34 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1S34 pdb_00001s34 10.2210/pdb1s34/pdb RCSB RCSB021306 ? ? WWPDB D_1000021306 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1S2F _pdbx_database_related.details 'Minimzed average structure from these lowest energy structures.' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1S34 _pdbx_database_status.recvd_initial_deposition_date 2004-01-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cabello-Villegas, J.' 1 'Giles, K.E.' 2 'Soto, A.M.' 3 'Yu, P.' 4 'Beemon, K.L.' 5 'Wang, Y.X.' 6 # _citation.id primary _citation.title ;Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor. ; _citation.journal_abbrev Rna _citation.journal_volume 10 _citation.page_first 1388 _citation.page_last 1398 _citation.year 2004 _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 15317975 _citation.pdbx_database_id_DOI 10.1261/rna.7020804 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cabello-Villegas, J.' 1 ? primary 'Giles, K.E.' 2 ? primary 'Soto, A.M.' 3 ? primary 'Yu, P.' 4 ? primary 'Mougin, A.' 5 ? primary 'Beemon, K.L.' 6 ? primary 'Wang, Y.X.' 7 ? # _cell.entry_id 1S34 _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S34 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-R(*GP*GP*GP*GP*AP*GP*UP*GP*GP*UP*UP*UP*GP*UP*AP*UP*CP*CP*UP*UP*CP*CP*C)-3'" _entity.formula_weight 7350.335 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ;Pseudo 5'-splice site ; _entity.details ? # _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 GGGGAGUGGUUUGUAUCCUUCCC _entity_poly.pdbx_seq_one_letter_code_can GGGGAGUGGUUUGUAUCCUUCCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # 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 G n 1 4 G n 1 5 A n 1 6 G n 1 7 U n 1 8 G n 1 9 G n 1 10 U n 1 11 U n 1 12 U n 1 13 G n 1 14 U n 1 15 A n 1 16 U n 1 17 C n 1 18 C n 1 19 U n 1 20 U n 1 21 C n 1 22 C n 1 23 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _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 'In vitro transcription' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1S34 _struct_ref.pdbx_db_accession 1S34 _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 1S34 _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 23 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1S34 _struct_ref_seq.db_align_beg 907 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 929 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 907 _struct_ref_seq.pdbx_auth_seq_align_end 929 # 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 3D_13C-separated_NOESY 3 1 1 DQF-COSY 4 1 1 HNN-COSY 5 2 2 '2D NOESY' 6 1 1 HCP # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 298 ambient 6.5 '25mM NaCl, 10 mM Sodium Phosphate' ? K 2 288 ambient 6.5 '25mM NaCl, 10 mM Sodium Phosphate' ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1 mM 23 mer RNA (NRS23)' '>99% D2O' 2 '1 mM NRS23' '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Bruker DRX 500 2 ? Varian INOVA 500 3 ? Varian INOVA 600 4 ? Varian INOVA 800 # _pdbx_nmr_refine.entry_id 1S34 _pdbx_nmr_refine.method ;Simulated annealing. Refinement using torsion angle dynamics and the DELPHIC database ; _pdbx_nmr_refine.details ;DELPHIC torsion angle potential was used for the whole molecule. The base position potential was excluded for residues 913, and 917 to 920. Protocol from Clore and Kuszewski (J Am Chem Soc. 2003. 125(6):1518-25) ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1S34 _pdbx_nmr_details.text ;RDC restraints were obtained for the base one bond H-C and H-N using HSQC experiments. RDC restraints for the ribose were obtained from measurements on an Relay HCCH-COSY (Vallurupalli and Moore, J Biomol NMR. 2002. 24(1):63-6). Anisotropic conditions were ~20 mg/ml pf1 phage. ; # _pdbx_nmr_ensemble.entry_id 1S34 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1S34 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal VNMR 6.1 collection varian 1 NMRPipe 4.1 processing 'F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax' 2 NMRDraw 4.1 'data analysis' 'Delaglio, F.' 3 NMRView 5.0.4 'data analysis' 'Johnson and Blevins' 4 X-PLOR 'NIH 2.0.6' 'structure solution' 'C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore' 5 X-PLOR 'NIH 2.0.6' refinement 'C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clore' 6 # _exptl.entry_id 1S34 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.density_Matthews ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1S34 _struct.title 'Solution structure of residues 907-929 from Rous Sarcoma Virus' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1S34 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'stem-loop, tetraloop, bulge, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _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 G 1 N1 ? ? ? 1_555 A C 23 N3 ? ? A G 907 A C 929 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 23 O2 ? ? A G 907 A C 929 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 23 N4 ? ? A G 907 A C 929 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 22 N3 ? ? A G 908 A C 928 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 22 O2 ? ? A G 908 A C 928 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 22 N4 ? ? A G 908 A C 928 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 909 A C 927 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 21 O2 ? ? A G 909 A C 927 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 21 N4 ? ? A G 909 A C 927 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A U 20 O2 ? ? A G 910 A U 926 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A U 20 N3 ? ? A G 910 A U 926 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 19 N3 ? ? A A 911 A U 925 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 19 O4 ? ? A A 911 A U 925 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 18 N3 ? ? A G 912 A C 924 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 18 O2 ? ? A G 912 A C 924 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 18 N4 ? ? A G 912 A C 924 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 8 N1 ? ? ? 1_555 A C 17 N3 ? ? A G 914 A C 923 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 8 N2 ? ? ? 1_555 A C 17 O2 ? ? A G 914 A C 923 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 8 O6 ? ? ? 1_555 A C 17 N4 ? ? A G 914 A C 923 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 A U 16 O2 ? ? A G 915 A U 922 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog21 hydrog ? ? A G 9 O6 ? ? ? 1_555 A U 16 N3 ? ? A G 915 A U 922 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog22 hydrog ? ? A U 10 N3 ? ? ? 1_555 A A 15 N1 ? ? A U 916 A A 921 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 10 O4 ? ? ? 1_555 A A 15 N6 ? ? A U 916 A A 921 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1S34 _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 # _atom_sites.entry_id 1S34 _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _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] 1.000000 _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 H N O P # 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 1 907 907 G G A . n A 1 2 G 2 908 908 G G A . n A 1 3 G 3 909 909 G G A . n A 1 4 G 4 910 910 G G A . n A 1 5 A 5 911 911 A A A . n A 1 6 G 6 912 912 G G A . n A 1 7 U 7 913 913 U U A . n A 1 8 G 8 914 914 G G A . n A 1 9 G 9 915 915 G G A . n A 1 10 U 10 916 916 U U A . n A 1 11 U 11 917 917 U U A . n A 1 12 U 12 918 918 U U A . n A 1 13 G 13 919 919 G G A . n A 1 14 U 14 920 920 U U A . n A 1 15 A 15 921 921 A A A . n A 1 16 U 16 922 922 U U A . n A 1 17 C 17 923 923 C C A . n A 1 18 C 18 924 924 C C A . n A 1 19 U 19 925 925 U U A . n A 1 20 U 20 926 926 U U A . n A 1 21 C 21 927 927 C C A . n A 1 22 C 22 928 928 C C A . n A 1 23 C 23 929 929 C C A . n # _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 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 2004-08-31 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # 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' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 2 "O2'" A U 917 ? ? "H5'" A U 918 ? ? 1.29 2 2 "HO2'" A U 917 ? ? "O4'" A U 918 ? ? 1.44 3 3 "HO2'" A U 916 ? ? "O5'" A U 917 ? ? 1.49 4 3 "O2'" A U 913 ? ? H8 A G 914 ? ? 1.58 5 3 "O2'" A U 920 ? ? "H5'" A A 921 ? ? 1.58 6 3 "O2'" A U 918 ? ? H8 A G 919 ? ? 1.58 7 4 "H5''" A U 920 ? ? "O4'" A A 921 ? ? 1.41 8 4 "O2'" A U 918 ? ? "H2'" A G 919 ? ? 1.59 9 5 "HO2'" A U 918 ? ? "O4'" A G 919 ? ? 1.48 10 5 "O2'" A U 917 ? ? H6 A U 918 ? ? 1.53 11 5 "HO2'" A U 917 ? ? OP2 A U 918 ? ? 1.60 12 6 "O2'" A U 917 ? ? "H5'" A U 918 ? ? 1.27 13 6 "HO2'" A U 917 ? ? "O4'" A U 918 ? ? 1.42 14 7 "O2'" A U 918 ? ? "H2'" A G 919 ? ? 1.39 15 8 "HO2'" A U 913 ? ? "O5'" A G 914 ? ? 1.56 16 11 "HO2'" A U 918 ? ? "O4'" A G 919 ? ? 1.36 17 11 "O2'" A U 918 ? ? "O4'" A G 919 ? ? 1.65 18 13 "O2'" A U 917 ? ? H6 A U 918 ? ? 1.32 19 13 "H3'" A G 919 ? ? "O4'" A U 920 ? ? 1.60 20 14 "O2'" A U 918 ? ? "H2'" A G 919 ? ? 1.44 21 14 "H5''" A U 920 ? ? "O4'" A A 921 ? ? 1.47 22 14 "HO2'" A U 918 ? ? "O5'" A G 919 ? ? 1.51 23 15 "H5''" A U 920 ? ? "O4'" A A 921 ? ? 1.55 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 3 "C4'" A U 917 ? ? "C3'" A U 917 ? ? 1.624 1.527 0.097 0.011 N 2 4 "C4'" A G 919 ? ? "C3'" A G 919 ? ? 1.447 1.521 -0.074 0.010 N 3 7 "C4'" A U 918 ? ? "C3'" A U 918 ? ? 1.427 1.521 -0.094 0.010 N 4 11 "C4'" A U 918 ? ? "C3'" A U 918 ? ? 1.444 1.521 -0.077 0.010 N 5 11 "C4'" A U 920 ? ? "C3'" A U 920 ? ? 1.430 1.521 -0.091 0.010 N 6 12 "C4'" A U 918 ? ? "C3'" A U 918 ? ? 1.443 1.521 -0.078 0.010 N 7 13 "C4'" A G 909 ? ? "C3'" A G 909 ? ? 1.605 1.527 0.078 0.011 N 8 14 "C4'" A U 918 ? ? "C3'" A U 918 ? ? 1.453 1.521 -0.068 0.010 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 "O4'" A G 919 ? ? "C4'" A G 919 ? ? "C3'" A G 919 ? ? 112.94 106.10 6.84 0.80 N 2 2 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 111.26 106.10 5.16 0.80 N 3 3 "C5'" A U 917 ? ? "C4'" A U 917 ? ? "C3'" A U 917 ? ? 104.57 115.20 -10.63 1.40 N 4 3 "O4'" A G 919 ? ? "C4'" A G 919 ? ? "C3'" A G 919 ? ? 112.83 106.10 6.73 0.80 N 5 4 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 111.33 106.10 5.23 0.80 N 6 5 "O4'" A G 919 ? ? "C4'" A G 919 ? ? "C3'" A G 919 ? ? 110.95 106.10 4.85 0.80 N 7 6 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 111.27 106.10 5.17 0.80 N 8 7 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 112.15 106.10 6.05 0.80 N 9 7 "O4'" A G 919 ? ? "C4'" A G 919 ? ? "C3'" A G 919 ? ? 112.14 106.10 6.04 0.80 N 10 11 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 110.95 106.10 4.85 0.80 N 11 13 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 111.02 106.10 4.92 0.80 N 12 14 "O4'" A U 918 ? ? "C4'" A U 918 ? ? "C3'" A U 918 ? ? 111.88 106.10 5.78 0.80 N 13 14 "O4'" A G 919 ? ? "C4'" A G 919 ? ? "C3'" A G 919 ? ? 111.07 106.10 4.97 0.80 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1S34 'a-form double helix' 1S34 'hairpin loop' 1S34 'bulge loop' 1S34 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 A C 23 1_555 0.513 -0.030 -0.128 -9.832 -14.665 -1.659 1 A_G907:C929_A A 907 ? A 929 ? 19 1 1 A G 2 1_555 A C 22 1_555 -0.258 -0.177 0.179 -4.646 -25.036 -2.630 2 A_G908:C928_A A 908 ? A 928 ? 19 1 1 A G 3 1_555 A C 21 1_555 -0.717 -0.262 0.264 -4.887 -10.190 -2.918 3 A_G909:C927_A A 909 ? A 927 ? 19 1 1 A G 4 1_555 A U 20 1_555 -1.877 -0.346 -0.188 -5.306 -13.868 0.038 4 A_G910:U926_A A 910 ? A 926 ? 28 1 1 A A 5 1_555 A U 19 1_555 -0.041 -0.079 -0.315 -4.725 -19.912 -0.152 5 A_A911:U925_A A 911 ? A 925 ? 20 1 1 A G 6 1_555 A C 18 1_555 0.047 -0.030 -0.257 1.507 -8.088 -1.927 6 A_G912:C924_A A 912 ? A 924 ? 19 1 1 A G 8 1_555 A C 17 1_555 -1.095 -0.467 -0.384 0.389 -13.939 2.098 7 A_G914:C923_A A 914 ? A 923 ? 19 1 1 A G 9 1_555 A U 16 1_555 -1.992 -0.384 -0.174 2.774 -11.994 0.022 8 A_G915:U922_A A 915 ? A 922 ? 28 1 1 A U 10 1_555 A A 15 1_555 0.194 -0.105 -0.849 12.784 -8.615 -1.401 9 A_U916:A921_A A 916 ? A 921 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 A C 23 1_555 A G 2 1_555 A C 22 1_555 -0.071 -1.807 2.852 -1.529 8.728 27.878 -5.080 -0.122 2.198 17.564 3.076 29.226 1 AA_G907G908:C928C929_AA A 907 ? A 929 ? A 908 ? A 928 ? 1 A G 2 1_555 A C 22 1_555 A G 3 1_555 A C 21 1_555 0.321 -1.921 3.145 -1.515 14.415 27.929 -5.777 -0.828 1.925 27.635 2.905 31.399 2 AA_G908G909:C927C928_AA A 908 ? A 928 ? A 909 ? A 927 ? 1 A G 3 1_555 A C 21 1_555 A G 4 1_555 A U 20 1_555 0.424 -2.039 3.130 0.862 11.463 26.534 -6.217 -0.691 2.099 23.616 -1.776 28.876 3 AA_G909G910:U926C927_AA A 909 ? A 927 ? A 910 ? A 926 ? 1 A G 4 1_555 A U 20 1_555 A A 5 1_555 A U 19 1_555 -0.053 -1.463 3.148 -0.358 9.502 39.778 -3.050 0.039 2.742 13.728 0.518 40.854 4 AA_G910A911:U925U926_AA A 910 ? A 926 ? A 911 ? A 925 ? 1 A A 5 1_555 A U 19 1_555 A G 6 1_555 A C 18 1_555 -0.253 -1.430 2.849 0.018 17.361 29.772 -4.486 0.430 1.771 30.723 -0.032 34.365 5 AA_A911G912:C924U925_AA A 911 ? A 925 ? A 912 ? A 924 ? 1 A G 6 1_555 A C 18 1_555 A G 8 1_555 A C 17 1_555 -2.261 -1.543 3.969 4.819 9.952 44.936 -2.928 3.347 3.326 12.792 -6.194 46.208 6 AA_G912G914:C923C924_AA A 912 ? A 924 ? A 914 ? A 923 ? 1 A G 8 1_555 A C 17 1_555 A G 9 1_555 A U 16 1_555 -0.345 -1.936 3.193 -4.214 4.687 26.339 -5.246 -0.260 2.832 10.102 9.082 27.070 7 AA_G914G915:U922C923_AA A 914 ? A 923 ? A 915 ? A 922 ? 1 A G 9 1_555 A U 16 1_555 A U 10 1_555 A A 15 1_555 -0.038 -1.166 2.987 1.054 8.265 38.710 -2.575 0.165 2.690 12.295 -1.568 39.563 8 AA_G915U916:A921U922_AA A 915 ? A 922 ? A 916 ? A 921 ? #