data_1K8S # _entry.id 1K8S # _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 1K8S pdb_00001k8s 10.2210/pdb1k8s/pdb RCSB RCSB014702 ? ? WWPDB D_1000014702 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1K8S _pdbx_database_status.recvd_initial_deposition_date 2001-10-25 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _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 'Thiviyanathan, V.' 1 'Guliaev, A.B.' 2 'Leontis, N.B.' 3 'Gorenstein, D.G.' 4 # _citation.id primary _citation.title 'Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 300 _citation.page_first 1143 _citation.page_last 1154 _citation.year 2000 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10903860 _citation.pdbx_database_id_DOI 10.1006/jmbi.2000.3931 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Thiviyanathan, V.' 1 ? primary 'Guliaev, A.B.' 2 ? primary 'Leontis, N.B.' 3 ? primary 'Gorenstein, D.G.' 4 ? # 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 "5'-R(*GP*GP*CP*AP*GP*AP*GP*UP*GP*CP*CP*GP*C)-3'" 4211.582 1 ? ? ? 'Bulged base RNA duplex E Coli 5S rRNA' 2 polymer syn "5'-R(*GP*CP*GP*GP*CP*AP*CP*CP*UP*GP*CP*C)-3'" 3802.328 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GGCAGAGUGCCGC GGCAGAGUGCCGC A ? 2 polyribonucleotide no no GCGGCACCUGCC GCGGCACCUGCC B ? # 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 C n 1 4 A n 1 5 G n 1 6 A n 1 7 G n 1 8 U n 1 9 G n 1 10 C n 1 11 C n 1 12 G n 1 13 C n 2 1 G n 2 2 C n 2 3 G n 2 4 G n 2 5 C n 2 6 A n 2 7 C n 2 8 C n 2 9 U n 2 10 G n 2 11 C n 2 12 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'Enzymatically synthesized using T7 RNA Polymerase.' 2 1 sample ? ? ? ? ? 'Enzymatically synthesized using T7 RNA Polymerase.' # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1K8S 1K8S ? ? ? 2 2 PDB 1K8S 1K8S ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1K8S A 1 ? 13 ? 1K8S 1 ? 13 ? 1 13 2 2 1K8S B 1 ? 12 ? 1K8S 14 ? 25 ? 14 25 # 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 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type '2D NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength '110 mM' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '100 mM NaCl, 10 mM sodium phosphate, 0.02 mM EDTA' _pdbx_nmr_sample_details.solvent_system D2O/H2O # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model VXRS _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1K8S _pdbx_nmr_refine.method ;matrix relaxation, molecular dynamics, torsion angle dynamics ; _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1K8S _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal Felix 95 'data analysis' MSI 1 MORASS 2.1 'iterative matrix relaxation' 'Meadows, Gorenstein et al.' 2 Amber 5.0 refinement UCSF 3 # _exptl.entry_id 1K8S _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _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 1K8S _struct.title 'BULGED ADENOSINE IN AN RNA DUPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1K8S _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Bulged base, bulged adenosine, bulged RNA, RNA bulges, 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_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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 2 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 2 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 2 B C 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 3 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 3 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 3 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 B U 9 N3 ? ? A A 4 B U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 B U 9 O4 ? ? A A 4 B U 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 5 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 5 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 5 B C 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 7 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 7 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 7 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 6 N1 ? ? A U 8 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 6 N6 ? ? A U 8 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 9 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 9 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 9 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 9 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 9 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 9 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 10 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 10 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 10 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 11 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 11 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 11 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 12 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 12 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 12 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 13 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 13 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 13 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1K8S _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 1K8S _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 1 1 G RG5 A . n A 1 2 G 2 2 2 G RG A . n A 1 3 C 3 3 3 C RC A . n A 1 4 A 4 4 4 A RA A . n A 1 5 G 5 5 5 G RG A . n A 1 6 A 6 6 6 A RA A . n A 1 7 G 7 7 7 G RG A . n A 1 8 U 8 8 8 U RU A . n A 1 9 G 9 9 9 G RG A . n A 1 10 C 10 10 10 C RC A . n A 1 11 C 11 11 11 C RC A . n A 1 12 G 12 12 12 G RG A . n A 1 13 C 13 13 13 C RC3 A . n B 2 1 G 1 14 14 G RG5 B . n B 2 2 C 2 15 15 C RC B . n B 2 3 G 3 16 16 G RG B . n B 2 4 G 4 17 17 G RG B . n B 2 5 C 5 18 18 C RC B . n B 2 6 A 6 19 19 A RA B . n B 2 7 C 7 20 20 C RC B . n B 2 8 C 8 21 21 C RC B . n B 2 9 U 9 22 22 U RU B . n B 2 10 G 10 23 23 G RG B . n B 2 11 C 11 24 24 C RC B . n B 2 12 C 12 25 25 C RC3 B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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 2001-11-14 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _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_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 1 ? ? "C1'" A G 1 ? ? N9 A G 1 ? ? 113.47 108.50 4.97 0.70 N 2 1 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 113.24 108.50 4.74 0.70 N 3 1 "O4'" A A 4 ? ? "C1'" A A 4 ? ? N9 A A 4 ? ? 112.91 108.50 4.41 0.70 N 4 1 C5 A A 6 ? ? C6 A A 6 ? ? N1 A A 6 ? ? 120.99 117.70 3.29 0.50 N 5 1 N1 A A 6 ? ? C6 A A 6 ? ? N6 A A 6 ? ? 114.49 118.60 -4.11 0.60 N 6 1 "O4'" A U 8 ? ? "C1'" A U 8 ? ? N1 A U 8 ? ? 115.09 108.50 6.59 0.70 N 7 1 "O4'" A C 11 ? ? "C1'" A C 11 ? ? N1 A C 11 ? ? 114.87 108.50 6.37 0.70 N 8 1 N3 A C 11 ? ? C2 A C 11 ? ? O2 A C 11 ? ? 117.59 121.90 -4.31 0.70 N 9 1 "O4'" A G 12 ? ? "C1'" A G 12 ? ? N9 A G 12 ? ? 112.97 108.50 4.47 0.70 N 10 1 "O4'" A C 13 ? ? "C1'" A C 13 ? ? N1 A C 13 ? ? 113.30 108.50 4.80 0.70 N 11 1 "C3'" B C 15 ? ? "C2'" B C 15 ? ? "C1'" B C 15 ? ? 107.42 101.50 5.92 0.80 N 12 1 "O4'" B C 15 ? ? "C1'" B C 15 ? ? N1 B C 15 ? ? 113.34 108.50 4.84 0.70 N 13 1 "O4'" B G 16 ? ? "C1'" B G 16 ? ? N9 B G 16 ? ? 113.12 108.50 4.62 0.70 N 14 1 "O4'" B C 18 ? ? "C1'" B C 18 ? ? N1 B C 18 ? ? 113.31 108.50 4.81 0.70 N 15 1 "O4'" B A 19 ? ? "C1'" B A 19 ? ? N9 B A 19 ? ? 112.72 108.50 4.22 0.70 N 16 1 N1 B A 19 ? ? C6 B A 19 ? ? N6 B A 19 ? ? 114.45 118.60 -4.15 0.60 N 17 1 "O4'" B C 20 ? ? "C1'" B C 20 ? ? N1 B C 20 ? ? 112.96 108.50 4.46 0.70 N 18 1 "C3'" B C 21 ? ? "C2'" B C 21 ? ? "C1'" B C 21 ? ? 106.65 101.50 5.15 0.80 N 19 1 "C3'" B U 22 ? ? "C2'" B U 22 ? ? "C1'" B U 22 ? ? 106.76 101.50 5.26 0.80 N 20 1 "O4'" B U 22 ? ? "C1'" B U 22 ? ? N1 B U 22 ? ? 113.65 108.50 5.15 0.70 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 4 ? ? 0.071 'SIDE CHAIN' 2 1 G A 7 ? ? 0.051 'SIDE CHAIN' 3 1 G A 9 ? ? 0.092 'SIDE CHAIN' 4 1 C A 11 ? ? 0.089 'SIDE CHAIN' 5 1 G A 12 ? ? 0.079 'SIDE CHAIN' 6 1 C A 13 ? ? 0.087 'SIDE CHAIN' 7 1 C B 20 ? ? 0.061 'SIDE CHAIN' 8 1 C B 21 ? ? 0.096 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1K8S 'double helix' 1K8S 'a-form double helix' 1K8S 'bulge loop' # 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 B C 12 1_555 -0.439 -0.234 -0.222 -7.155 3.286 -0.662 1 A_G1:C25_B A 1 ? B 25 ? 19 1 1 A G 2 1_555 B C 11 1_555 -0.267 -0.155 0.126 2.275 -6.351 0.373 2 A_G2:C24_B A 2 ? B 24 ? 19 1 1 A C 3 1_555 B G 10 1_555 0.548 -0.272 -0.103 2.881 -15.578 0.310 3 A_C3:G23_B A 3 ? B 23 ? 19 1 1 A A 4 1_555 B U 9 1_555 -0.112 -0.089 -0.108 -15.588 -13.630 0.583 4 A_A4:U22_B A 4 ? B 22 ? 20 1 1 A G 5 1_555 B C 8 1_555 -0.318 -0.189 -0.157 -10.459 -19.144 -1.259 5 A_G5:C21_B A 5 ? B 21 ? 19 1 1 A G 7 1_555 B C 7 1_555 -0.321 -0.162 0.098 -17.716 -19.435 0.348 6 A_G7:C20_B A 7 ? B 20 ? 19 1 1 A U 8 1_555 B A 6 1_555 0.004 -0.143 0.873 -11.636 -0.894 4.834 7 A_U8:A19_B A 8 ? B 19 ? 20 1 1 A G 9 1_555 B C 5 1_555 -0.475 -0.261 0.250 5.892 -19.264 -0.340 8 A_G9:C18_B A 9 ? B 18 ? 19 1 1 A C 10 1_555 B G 4 1_555 0.370 -0.213 0.353 -3.253 -15.494 -0.539 9 A_C10:G17_B A 10 ? B 17 ? 19 1 1 A C 11 1_555 B G 3 1_555 0.316 -0.231 0.070 -0.738 -24.110 -0.446 10 A_C11:G16_B A 11 ? B 16 ? 19 1 1 A G 12 1_555 B C 2 1_555 -0.632 -0.239 -0.937 -24.806 -29.070 7.363 11 A_G12:C15_B A 12 ? B 15 ? 19 1 1 A C 13 1_555 B G 1 1_555 0.489 -0.125 0.469 -24.615 12.521 2.101 12 A_C13:G14_B A 13 ? B 14 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 12 1_555 A G 2 1_555 B C 11 1_555 0.730 -1.574 3.034 -0.897 5.808 29.716 -4.045 -1.558 2.662 11.188 1.729 30.279 1 AA_G1G2:C24C25_BB A 1 ? B 25 ? A 2 ? B 24 ? 1 A G 2 1_555 B C 11 1_555 A C 3 1_555 B G 10 1_555 -0.261 -1.468 3.254 2.771 1.231 38.797 -2.350 0.723 3.183 1.850 -4.164 38.911 2 AA_G2C3:G23C24_BB A 2 ? B 24 ? A 3 ? B 23 ? 1 A C 3 1_555 B G 10 1_555 A A 4 1_555 B U 9 1_555 0.584 -1.335 3.484 2.208 14.476 33.644 -4.103 -0.628 2.732 23.667 -3.610 36.608 3 AA_C3A4:U22G23_BB A 3 ? B 23 ? A 4 ? B 22 ? 1 A A 4 1_555 B U 9 1_555 A G 5 1_555 B C 8 1_555 -0.498 -1.299 3.127 -0.707 9.586 30.488 -3.927 0.790 2.619 17.684 1.304 31.933 4 AA_A4G5:C21U22_BB A 4 ? B 22 ? A 5 ? B 21 ? 1 A G 5 1_555 B C 8 1_555 A G 7 1_555 B C 7 1_555 -1.867 -1.279 5.388 21.207 16.254 52.172 -2.618 3.621 3.908 17.260 -22.519 58.187 5 AA_G5G7:C20C21_BB A 5 ? B 21 ? A 7 ? B 20 ? 1 A G 7 1_555 B C 7 1_555 A U 8 1_555 B A 6 1_555 0.183 -0.989 3.142 -8.535 0.310 33.385 -1.716 -1.576 2.996 0.529 14.562 34.430 6 AA_G7U8:A19C20_BB A 7 ? B 20 ? A 8 ? B 19 ? 1 A U 8 1_555 B A 6 1_555 A G 9 1_555 B C 5 1_555 -0.756 -1.497 2.566 2.285 4.167 28.398 -3.705 1.901 2.261 8.420 -4.617 28.785 7 AA_U8G9:C18A19_BB A 8 ? B 19 ? A 9 ? B 18 ? 1 A G 9 1_555 B C 5 1_555 A C 10 1_555 B G 4 1_555 -0.231 -1.566 3.414 -4.766 3.440 37.230 -2.883 -0.277 3.265 5.347 7.408 37.675 8 AA_G9C10:G17C18_BB A 9 ? B 18 ? A 10 ? B 17 ? 1 A C 10 1_555 B G 4 1_555 A C 11 1_555 B G 3 1_555 0.762 -1.779 3.134 4.623 4.286 29.166 -4.294 -0.576 2.932 8.387 -9.048 29.826 9 AA_C10C11:G16G17_BB A 10 ? B 17 ? A 11 ? B 16 ? 1 A C 11 1_555 B G 3 1_555 A G 12 1_555 B C 2 1_555 0.315 -1.124 3.794 9.608 33.575 22.778 -5.264 0.607 1.289 55.647 -15.924 41.499 10 AA_C11G12:C15G16_BB A 11 ? B 16 ? A 12 ? B 15 ? 1 A G 12 1_555 B C 2 1_555 A C 13 1_555 B G 1 1_555 0.182 -0.758 3.470 -13.045 2.907 30.010 -1.864 -2.663 3.047 5.296 23.766 32.789 11 AA_G12C13:G14C15_BB A 12 ? B 15 ? A 13 ? B 14 ? #