data_2AP5 # _entry.id 2AP5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 2AP5 pdb_00002ap5 10.2210/pdb2ap5/pdb RCSB RCSB034153 ? ? WWPDB D_1000034153 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2AP0 _pdbx_database_related.details '20 lowest energy structures' _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 2AP5 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.recvd_initial_deposition_date 2005-08-15 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry N _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cornish, P.V.' 1 'Giedroc, D.P.' 2 # _citation.id primary _citation.title 'The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical' _citation.journal_abbrev Rna _citation.journal_volume 12 _citation.page_first 1959 _citation.page_last 1969 _citation.year 2006 _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 17000902 _citation.pdbx_database_id_DOI 10.1261/rna.199006 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cornish, P.V.' 1 ? primary 'Stammler, S.N.' 2 ? primary 'Giedroc, D.P.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'C27A Sugarcane Yellow Leaf Virus RNA pseudoknot' _entity.formula_weight 9024.501 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'AGUGG(CH)GCCGACCACUUAAAAACAACGG' _entity_poly.pdbx_seq_one_letter_code_can AGUGGCGCCGACCACUUAAAAACAACGG _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 A n 1 2 G n 1 3 U n 1 4 G n 1 5 G n 1 6 CH n 1 7 G n 1 8 C n 1 9 C n 1 10 G n 1 11 A n 1 12 C n 1 13 C n 1 14 A n 1 15 C n 1 16 U n 1 17 U n 1 18 A n 1 19 A n 1 20 A n 1 21 A n 1 22 A n 1 23 C n 1 24 A n 1 25 A n 1 26 C n 1 27 G n 1 28 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 'Mutant of naturally occuring RNA fragment that forms an RNA pseudoknot in Sugarcane Yellow Leaf Virus' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2AP5 _struct_ref.pdbx_db_accession 2AP5 _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 2AP5 _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 28 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2AP5 _struct_ref_seq.db_align_beg 3 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 30 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 3 _struct_ref_seq.pdbx_auth_seq_align_end 30 # 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 CH 'RNA linking' n ;N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE ; ? 'C9 H15 N3 O8 P 1' 324.204 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.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 '2D NOESY' 1 2 2 '2D NOESY' 2 3 2 '2D TOCSY' 2 4 2 TROSY 3 # 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 1 283 ambient 6.0 '100mM KCl, 5mM MgCl2' . K 2 298 ambient 6.0 '100mM KCl, 5mM MgCl2' . K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '2.7mM C27A ScYLV, 100mM KCl, 5mM MgCl2' '90% H2O/10% D2O' 2 '2.7mM C27A ScYLV, 100mM KCl, 5mM MgCl2' '100% D2O' 3 '2.7mM C27A ScYLV, 100mM KCl, 5mM MgCl2, 15 mg/ml PF1 phage' '100% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.type ? # _pdbx_nmr_refine.entry_id 2AP5 _pdbx_nmr_refine.method ;simulated annealing starting with random coordinates followed by refinement with residual dipolar couplings ; _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 2AP5 _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # _pdbx_nmr_representative.entry_id 2AP5 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal processing NMRPipe 'Mac OS X version' 'F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax' 1 'data analysis' Sparky 3 'T. D. Goddard and D. G. Kneller' 2 'structure solution' XPLOR-NIH 2.10 'G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandra' 3 refinement XPLOR-NIH 2.10 'G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandra' 4 # _exptl.entry_id 2AP5 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 2AP5 _struct.title 'Solution Structure of the C27A ScYLV P1-P2 Frameshifting Pseudoknot, Average Structure' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2AP5 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA pseudoknot; frameshifting, 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 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 5 "O3'" ? ? ? 1_555 A CH 6 P ? ? A G 7 A CH 8 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale both ? A CH 6 "O3'" ? ? ? 1_555 A G 7 P ? ? A CH 8 A G 9 1_555 ? ? ? ? ? ? ? 1.612 ? ? hydrog1 hydrog ? ? A A 1 N1 ? ? ? 1_555 A U 16 N3 ? ? A A 3 A U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A A 1 N6 ? ? ? 1_555 A U 16 O4 ? ? A A 3 A U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 15 N3 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 15 O2 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 15 N4 ? ? A G 4 A C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 A A 14 N1 ? ? A U 5 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 A A 14 N6 ? ? A U 5 A A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 6 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 6 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 6 A C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N3 ? ? ? 1_555 A A 21 N6 ? ? A G 6 A A 23 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 12 N3 ? ? A G 7 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 12 O2 ? ? A G 7 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 12 N4 ? ? A G 7 A C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 N2 ? ? ? 1_555 A A 24 N1 ? ? A G 7 A A 26 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog16 hydrog ? ? A G 5 N3 ? ? ? 1_555 A A 24 N6 ? ? A G 7 A A 26 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog17 hydrog ? ? A CH 6 N4 ? ? ? 1_555 A G 10 N7 ? ? A CH 8 A G 12 1_555 ? ? ? ? ? ? 'CH-G PAIR' ? ? ? hydrog18 hydrog ? ? A CH 6 O2 ? ? ? 1_555 A C 26 N4 ? ? A CH 8 A C 28 1_555 ? ? ? ? ? ? 'CH-C MISPAIR' ? ? ? hydrog19 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 28 N1 ? ? A C 10 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 28 O6 ? ? A C 10 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 28 N2 ? ? A C 10 A G 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 27 N1 ? ? A C 11 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 27 O6 ? ? A C 11 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 27 N2 ? ? A C 11 A G 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 26 N3 ? ? A G 12 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 26 O2 ? ? A G 12 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 26 N4 ? ? A G 12 A C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 12 O2 ? ? ? 1_555 A A 25 N6 ? ? A C 14 A A 27 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 A A 22 N6 ? ? A C 15 A A 24 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog30 hydrog ? ? A A 14 N3 ? ? ? 1_555 A A 20 N6 ? ? A A 16 A A 22 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog31 hydrog ? ? A C 15 O2 ? ? ? 1_555 A A 19 N6 ? ? A C 17 A A 21 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2AP5 _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 A 1 3 3 A A A . n A 1 2 G 2 4 4 G G A . n A 1 3 U 3 5 5 U U A . n A 1 4 G 4 6 6 G G A . n A 1 5 G 5 7 7 G G A . n A 1 6 CH 6 8 8 CH CH A . n A 1 7 G 7 9 9 G G A . n A 1 8 C 8 10 10 C C A . n A 1 9 C 9 11 11 C C A . n A 1 10 G 10 12 12 G G A . n A 1 11 A 11 13 13 A A A . n A 1 12 C 12 14 14 C C A . n A 1 13 C 13 15 15 C C A . n A 1 14 A 14 16 16 A A A . n A 1 15 C 15 17 17 C C A . n A 1 16 U 16 18 18 U U A . n A 1 17 U 17 19 19 U U A . n A 1 18 A 18 20 20 A A A . n A 1 19 A 19 21 21 A A A . n A 1 20 A 20 22 22 A A A . n A 1 21 A 21 23 23 A A A . n A 1 22 A 22 24 24 A A A . n A 1 23 C 23 25 25 C C A . n A 1 24 A 24 26 26 A A A . n A 1 25 A 25 27 27 A A A . n A 1 26 C 26 28 28 C C A . n A 1 27 G 27 29 29 G G A . n A 1 28 G 28 30 30 G G A . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id CH _pdbx_struct_mod_residue.label_seq_id 6 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id CH _pdbx_struct_mod_residue.auth_seq_id 8 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id C _pdbx_struct_mod_residue.details ;N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE ; # _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 2006-09-05 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _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' 'Database references' 4 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_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 H22 A G 6 ? ? H62 A A 24 ? ? 1.28 2 1 "H2'" A G 4 ? ? "O4'" A U 5 ? ? 1.55 3 1 "O2'" A A 21 ? ? H8 A A 22 ? ? 1.57 4 1 "HO2'" A A 26 ? ? "O4'" A A 27 ? ? 1.59 5 1 "HO2'" A A 21 ? ? OP2 A A 22 ? ? 1.59 6 1 "O2'" A A 24 ? ? "O4'" A A 26 ? ? 2.09 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A C 14 ? ? "C1'" A C 14 ? ? 1.473 1.526 -0.053 0.008 N 2 1 "C2'" A U 18 ? ? "C1'" A U 18 ? ? 1.426 1.526 -0.100 0.008 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.69 113.80 3.89 0.50 N 2 1 C8 A A 3 ? ? N9 A A 3 ? ? C4 A A 3 ? ? 103.27 105.80 -2.53 0.40 N 3 1 N7 A G 4 ? ? C8 A G 4 ? ? N9 A G 4 ? ? 118.01 113.10 4.91 0.50 N 4 1 C8 A G 4 ? ? N9 A G 4 ? ? C4 A G 4 ? ? 103.07 106.40 -3.33 0.40 N 5 1 N7 A G 6 ? ? C8 A G 6 ? ? N9 A G 6 ? ? 117.77 113.10 4.67 0.50 N 6 1 C8 A G 6 ? ? N9 A G 6 ? ? C4 A G 6 ? ? 103.30 106.40 -3.10 0.40 N 7 1 N7 A G 7 ? ? C8 A G 7 ? ? N9 A G 7 ? ? 117.94 113.10 4.84 0.50 N 8 1 C8 A G 7 ? ? N9 A G 7 ? ? C4 A G 7 ? ? 103.33 106.40 -3.07 0.40 N 9 1 N7 A G 9 ? ? C8 A G 9 ? ? N9 A G 9 ? ? 117.75 113.10 4.65 0.50 N 10 1 C8 A G 9 ? ? N9 A G 9 ? ? C4 A G 9 ? ? 103.68 106.40 -2.72 0.40 N 11 1 N7 A G 12 ? ? C8 A G 12 ? ? N9 A G 12 ? ? 117.71 113.10 4.61 0.50 N 12 1 C8 A G 12 ? ? N9 A G 12 ? ? C4 A G 12 ? ? 103.16 106.40 -3.24 0.40 N 13 1 "C3'" A A 13 ? ? "C2'" A A 13 ? ? "C1'" A A 13 ? ? 106.37 101.50 4.87 0.80 N 14 1 N7 A A 13 ? ? C8 A A 13 ? ? N9 A A 13 ? ? 117.52 113.80 3.72 0.50 N 15 1 N7 A A 16 ? ? C8 A A 16 ? ? N9 A A 16 ? ? 117.75 113.80 3.95 0.50 N 16 1 C8 A A 16 ? ? N9 A A 16 ? ? C4 A A 16 ? ? 102.93 105.80 -2.87 0.40 N 17 1 "O4'" A U 19 ? ? "C1'" A U 19 ? ? N1 A U 19 ? ? 113.03 108.50 4.53 0.70 N 18 1 "C3'" A A 20 ? ? "C2'" A A 20 ? ? "C1'" A A 20 ? ? 106.63 101.50 5.13 0.80 N 19 1 N7 A A 20 ? ? C8 A A 20 ? ? N9 A A 20 ? ? 117.53 113.80 3.73 0.50 N 20 1 "C1'" A A 21 ? ? "O4'" A A 21 ? ? "C4'" A A 21 ? ? 104.92 109.70 -4.78 0.70 N 21 1 "O4'" A A 21 ? ? "C1'" A A 21 ? ? N9 A A 21 ? ? 113.30 108.50 4.80 0.70 N 22 1 N7 A A 21 ? ? C8 A A 21 ? ? N9 A A 21 ? ? 117.56 113.80 3.76 0.50 N 23 1 N7 A A 22 ? ? C8 A A 22 ? ? N9 A A 22 ? ? 117.50 113.80 3.70 0.50 N 24 1 N7 A A 23 ? ? C8 A A 23 ? ? N9 A A 23 ? ? 117.06 113.80 3.26 0.50 N 25 1 C8 A A 23 ? ? N9 A A 23 ? ? C4 A A 23 ? ? 103.01 105.80 -2.79 0.40 N 26 1 N7 A A 24 ? ? C8 A A 24 ? ? N9 A A 24 ? ? 117.21 113.80 3.41 0.50 N 27 1 C8 A A 24 ? ? N9 A A 24 ? ? C4 A A 24 ? ? 102.31 105.80 -3.49 0.40 N 28 1 "C3'" A C 25 ? ? "C2'" A C 25 ? ? "C1'" A C 25 ? ? 106.44 101.50 4.94 0.80 N 29 1 N7 A A 26 ? ? C8 A A 26 ? ? N9 A A 26 ? ? 117.48 113.80 3.68 0.50 N 30 1 C8 A A 26 ? ? N9 A A 26 ? ? C4 A A 26 ? ? 103.27 105.80 -2.53 0.40 N 31 1 N7 A A 27 ? ? C8 A A 27 ? ? N9 A A 27 ? ? 117.37 113.80 3.57 0.50 N 32 1 C8 A A 27 ? ? N9 A A 27 ? ? C4 A A 27 ? ? 103.22 105.80 -2.58 0.40 N 33 1 N7 A G 29 ? ? C8 A G 29 ? ? N9 A G 29 ? ? 117.85 113.10 4.75 0.50 N 34 1 C8 A G 29 ? ? N9 A G 29 ? ? C4 A G 29 ? ? 103.38 106.40 -3.02 0.40 N 35 1 N7 A G 30 ? ? C8 A G 30 ? ? N9 A G 30 ? ? 117.93 113.10 4.83 0.50 N 36 1 C8 A G 30 ? ? N9 A G 30 ? ? C4 A G 30 ? ? 103.08 106.40 -3.32 0.40 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 A A 3 ? ? 0.061 'SIDE CHAIN' 2 1 G A 4 ? ? 0.073 'SIDE CHAIN' 3 1 U A 5 ? ? 0.070 'SIDE CHAIN' 4 1 G A 6 ? ? 0.077 'SIDE CHAIN' 5 1 G A 7 ? ? 0.061 'SIDE CHAIN' 6 1 C A 10 ? ? 0.066 'SIDE CHAIN' 7 1 C A 11 ? ? 0.058 'SIDE CHAIN' 8 1 G A 12 ? ? 0.077 'SIDE CHAIN' 9 1 C A 14 ? ? 0.065 'SIDE CHAIN' 10 1 C A 15 ? ? 0.081 'SIDE CHAIN' 11 1 A A 16 ? ? 0.085 'SIDE CHAIN' 12 1 C A 17 ? ? 0.063 'SIDE CHAIN' 13 1 U A 18 ? ? 0.086 'SIDE CHAIN' 14 1 G A 29 ? ? 0.063 'SIDE CHAIN' 15 1 G A 30 ? ? 0.084 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2AP5 'double helix' 2AP5 'a-form double helix' 2AP5 '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 A 1 1_555 A U 16 1_555 0.012 -0.125 -0.006 0.217 -1.058 1.064 1 A_A3:U18_A A 3 ? A 18 ? 20 1 1 A G 2 1_555 A C 15 1_555 -0.127 -0.101 -0.029 -0.150 -0.215 -1.864 2 A_G4:C17_A A 4 ? A 17 ? 19 1 1 A U 3 1_555 A A 14 1_555 -0.020 -0.121 0.008 -0.365 -0.282 0.621 3 A_U5:A16_A A 5 ? A 16 ? 20 1 1 A G 4 1_555 A C 13 1_555 -0.063 -0.102 0.016 0.286 -0.282 -1.942 4 A_G6:C15_A A 6 ? A 15 ? 19 1 1 A G 5 1_555 A C 12 1_555 -0.048 -0.098 0.020 0.409 -0.353 -2.530 5 A_G7:C14_A A 7 ? A 14 ? 19 1 1 A C 26 1_555 A G 10 1_555 0.116 -0.085 0.221 -16.555 -5.625 -1.258 6 A_C28:G12_A A 28 ? A 12 ? 19 1 1 A G 27 1_555 A C 9 1_555 -0.117 -0.109 0.011 0.336 -0.167 -1.625 7 A_G29:C11_A A 29 ? A 11 ? 19 1 1 A G 28 1_555 A C 8 1_555 -0.128 -0.099 0.018 0.466 0.022 -1.151 8 A_G30:C10_A A 30 ? A 10 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A A 1 1_555 A U 16 1_555 A G 2 1_555 A C 15 1_555 -0.502 -1.132 2.725 -0.517 22.581 36.325 -3.264 0.652 1.766 32.637 0.747 42.573 1 AA_A3G4:C17U18_AA A 3 ? A 18 ? A 4 ? A 17 ? 1 A G 2 1_555 A C 15 1_555 A U 3 1_555 A A 14 1_555 0.435 -1.185 2.886 -2.333 4.717 25.118 -3.792 -1.536 2.573 10.696 5.290 25.655 2 AA_G4U5:A16C17_AA A 4 ? A 17 ? A 5 ? A 16 ? 1 A U 3 1_555 A A 14 1_555 A G 4 1_555 A C 13 1_555 0.023 -0.471 3.124 1.060 15.521 34.388 -2.605 0.092 2.674 24.744 -1.690 37.646 3 AA_U5G6:C15A16_AA A 5 ? A 16 ? A 6 ? A 15 ? 1 A G 4 1_555 A C 13 1_555 A G 5 1_555 A C 12 1_555 1.130 -1.437 3.434 1.370 -0.880 24.384 -3.102 -2.216 3.540 -2.080 -3.238 24.438 4 AA_G6G7:C14C15_AA A 6 ? A 15 ? A 7 ? A 14 ? 1 A G 5 1_555 A C 12 1_555 A C 26 1_555 A G 10 1_555 -4.555 0.124 4.717 6.853 0.349 113.971 0.068 2.821 4.537 0.208 -4.084 114.104 5 AA_G7C28:G12C14_AA A 7 ? A 14 ? A 28 ? A 12 ? 1 A C 26 1_555 A G 10 1_555 A G 27 1_555 A C 9 1_555 -0.015 -1.872 2.460 -5.861 2.228 28.083 -4.134 -0.931 2.264 4.520 11.891 28.761 6 AA_C28G29:C11G12_AA A 28 ? A 12 ? A 29 ? A 11 ? 1 A G 27 1_555 A C 9 1_555 A G 28 1_555 A C 8 1_555 -0.285 -0.581 3.399 6.781 24.510 34.280 -3.273 1.077 2.397 36.084 -9.984 42.454 7 AA_G29G30:C10C11_AA A 29 ? A 11 ? A 30 ? A 10 ? #