data_1FC8 # _entry.id 1FC8 # _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 1FC8 pdb_00001fc8 10.2210/pdb1fc8/pdb RCSB RCSB011473 ? ? WWPDB D_1000011473 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1FC8 _pdbx_database_status.recvd_initial_deposition_date 2000-07-18 _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 'Trempe, J.-F.' 1 'Gehring, K.' 2 # _citation.id primary _citation.title ;NMR solution structure of an oligonucleotide hairpin with a 2'F-ANA/RNA stem: implications for RNase H specificity toward DNA/RNA hybrid duplexes. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 123 _citation.page_first 4896 _citation.page_last 4903 _citation.year 2001 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11457316 _citation.pdbx_database_id_DOI 10.1021/ja003859p # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Trempe, J.F.' 1 ? primary 'Wilds, C.J.' 2 ? primary 'Denisov, A.Y.' 3 ? primary 'Pon, R.T.' 4 ? primary 'Damha, M.J.' 5 ? primary 'Gehring, K.' 6 ? # _cell.entry_id 1FC8 _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 1FC8 _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*AP*CP)D(*TP*TP*CP*GP*(GFL)P*(TAF)P*(CFL)P*(CFL))-3'" _entity.formula_weight 3790.341 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name ;RNA/2'F-ANA HAIRPIN ; # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GGAC(DT)(DT)(DC)(DG)(GFL)(TAF)(CFL)(CFL)' _entity_poly.pdbx_seq_one_letter_code_can GGACTTCGGTCC _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 A n 1 4 C n 1 5 DT n 1 6 DT n 1 7 DC n 1 8 DG n 1 9 GFL n 1 10 TAF n 1 11 CFL n 1 12 CFL 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 'SOLID PHASE SYNTHESIS; PHOSPHORAMIDITE CHEMISTRY' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1FC8 _struct_ref.pdbx_db_accession 1FC8 _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 1FC8 _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1FC8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 12 # 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 CFL 'DNA linking' n '4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one' "2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" 'C9 H13 F N3 O7 P' 325.188 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GFL 'DNA linking' n '2-AMINO-9-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE' "2'-FLUORO-2-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" 'C10 H13 F N5 O7 P' 365.212 TAF 'DNA linking' n ;2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'-PHOSPHATE ; ? 'C10 H14 F N2 O8 P' 340.199 # 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 1 '2D NOESY' 2 3 1 DQF-COSY 2 4 1 '2D 1H-13C HMQC' 2 5 1 '2D 1H-31P HETCOR' 2 6 1 '2D 1H-19F HETCOR' 2 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7.2 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.066 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 ;0.5 mM Oligonucleotide hairpin; 90% H2O, 10% D2O ; '90% H2O/10% D2O' 2 ;0.5 mM Oligonucleotide hairpin; D2O ; D2O # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.type 1 DRX Bruker 500 ? 2 DMX Bruker 400 ? 3 UNITYPLUS Varian 750 ? # _pdbx_nmr_refine.entry_id 1FC8 _pdbx_nmr_refine.method ;Distance geometry, simulated annealing ; _pdbx_nmr_refine.details ;SA at 15000K for 15 psec from random coordinates. Refinement from lower energy structure at 3000K fro 9 psec. 5 structures generated. Total of 305 restraints: 98 intraresidue NOE-derived distance constraints, 94 sequential NOE-derived distance constraints, 3 long range NOE-derived distance constraints, 15 distance restraints from hydrogen bonds, 91 dihedral angle restraints, 4 planarity constraints for base pairs ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1FC8 _pdbx_nmr_details.text 'This structure was determined using standard 2D homonuclear techniques.' # _pdbx_nmr_ensemble.entry_id 1FC8 _pdbx_nmr_ensemble.conformers_calculated_total_number 5 _pdbx_nmr_ensemble.conformers_submitted_total_number 5 _pdbx_nmr_ensemble.conformer_selection_criteria 'RMSD FROM AVERAGE LOWER THAN 0.7 ANGSTROM' _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 1FC8 _pdbx_nmr_representative.conformer_id 3 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'structure solution' X-PLOR 3.843 BRUNGER 1 refinement X-PLOR 3.843 BRUNGER 2 # _exptl.entry_id 1FC8 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1FC8 _struct.title ;NMR SOLUTION STRUCTURE OF A CHIMERIC OLIGONUCLEOTIDE HAIRPIN R(GGAC)D(TTCG)2'F-A(GTCC) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1FC8 _struct_keywords.pdbx_keywords 'RNA/DNA CHIMERA' _struct_keywords.text ;2'F-ARABINONUCLEIC ACID, RNA, DNA, HYBRID DUPLEX, HAIRPIN, RNA-DNA CHIMERA COMPLEX ; # _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 DG 8 "O3'" ? ? ? 1_555 A GFL 9 P ? ? A DG 8 A GFL 9 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale2 covale one ? A GFL 9 "O3'" ? ? ? 1_555 A TAF 10 P ? ? A GFL 9 A TAF 10 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale3 covale one ? A TAF 10 "O3'" ? ? ? 1_555 A CFL 11 P ? ? A TAF 10 A CFL 11 1_555 ? ? ? ? ? ? ? 1.622 ? ? covale4 covale one ? A CFL 11 "O3'" ? ? ? 1_555 A CFL 12 P ? ? A CFL 11 A CFL 12 1_555 ? ? ? ? ? ? ? 1.616 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A CFL 12 N3 ? ? A G 1 A CFL 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A CFL 12 O2 ? ? A G 1 A CFL 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A CFL 12 N4 ? ? A G 1 A CFL 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A CFL 11 N3 ? ? A G 2 A CFL 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A CFL 11 O2 ? ? A G 2 A CFL 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A CFL 11 N4 ? ? A G 2 A CFL 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 A TAF 10 N3 ? ? A A 3 A TAF 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 A TAF 10 O4 ? ? A A 3 A TAF 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 4 N3 ? ? ? 1_555 A GFL 9 N1 ? ? A C 4 A GFL 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N4 ? ? ? 1_555 A GFL 9 O6 ? ? A C 4 A GFL 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 O2 ? ? ? 1_555 A GFL 9 N2 ? ? A C 4 A GFL 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O2 ? ? ? 1_555 A GFL 9 N1 ? ? A DT 5 A GFL 9 1_555 ? ? ? ? ? ? 'DT-GFL MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1FC8 _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 1FC8 _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 F 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 G A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 C 4 4 4 C C A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 GFL 9 9 9 GFL +G A . n A 1 10 TAF 10 10 10 TAF +T A . n A 1 11 CFL 11 11 11 CFL +C A . n A 1 12 CFL 12 12 12 CFL +C A . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A GFL 9 A GFL 9 ? DG ? 2 A TAF 10 A TAF 10 ? DT ? 3 A CFL 11 A CFL 11 ? DC ? 4 A CFL 12 A CFL 12 ? DC ? # _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 2001-05-30 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' '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 2 "HO2'" A C 4 ? ? "O4'" A DT 5 ? ? 1.56 2 3 O2 A DT 6 ? ? H22 A DG 8 ? ? 1.60 # 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 G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.82 113.10 4.72 0.50 N 2 1 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.88 106.40 -2.52 0.40 N 3 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.81 113.10 4.71 0.50 N 4 1 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.68 106.40 -2.72 0.40 N 5 1 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.48 113.80 3.68 0.50 N 6 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.53 108.30 2.23 0.30 N 7 1 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 110.54 108.30 2.24 0.30 N 8 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.49 108.30 2.19 0.30 N 9 1 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 118.06 113.10 4.96 0.50 N 10 2 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.78 113.10 4.68 0.50 N 11 2 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.94 106.40 -2.46 0.40 N 12 2 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.86 113.10 4.76 0.50 N 13 2 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.78 106.40 -2.62 0.40 N 14 2 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.56 113.80 3.76 0.50 N 15 2 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 110.31 108.30 2.01 0.30 N 16 2 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.90 108.30 2.60 0.30 N 17 2 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 118.03 113.10 4.93 0.50 N 18 3 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.77 113.10 4.67 0.50 N 19 3 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.88 106.40 -2.52 0.40 N 20 3 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.69 113.10 4.59 0.50 N 21 3 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.72 106.40 -2.68 0.40 N 22 3 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.54 113.80 3.74 0.50 N 23 3 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 111.01 108.30 2.71 0.30 N 24 3 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 110.94 108.30 2.64 0.30 N 25 3 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.69 108.30 2.39 0.30 N 26 3 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 117.98 113.10 4.88 0.50 N 27 3 C8 A DG 8 ? ? N9 A DG 8 ? ? C4 A DG 8 ? ? 103.93 106.40 -2.47 0.40 N 28 4 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.80 113.10 4.70 0.50 N 29 4 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.86 106.40 -2.54 0.40 N 30 4 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.73 113.10 4.63 0.50 N 31 4 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.70 106.40 -2.70 0.40 N 32 4 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.47 113.80 3.67 0.50 N 33 4 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.27 108.30 1.97 0.30 N 34 4 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 111.18 108.30 2.88 0.30 N 35 4 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.47 108.30 3.17 0.30 N 36 4 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 117.93 113.10 4.83 0.50 N 37 5 N7 A G 1 ? ? C8 A G 1 ? ? N9 A G 1 ? ? 117.66 113.10 4.56 0.50 N 38 5 C8 A G 1 ? ? N9 A G 1 ? ? C4 A G 1 ? ? 103.90 106.40 -2.50 0.40 N 39 5 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 117.63 113.10 4.53 0.50 N 40 5 C8 A G 2 ? ? N9 A G 2 ? ? C4 A G 2 ? ? 103.73 106.40 -2.67 0.40 N 41 5 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.56 113.80 3.76 0.50 N 42 5 "O4'" A C 4 ? ? "C1'" A C 4 ? ? N1 A C 4 ? ? 112.71 108.50 4.21 0.70 N 43 5 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.31 108.30 2.01 0.30 N 44 5 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 110.19 108.30 1.89 0.30 N 45 5 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 110.74 108.30 2.44 0.30 N 46 5 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.45 108.30 3.15 0.30 N 47 5 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 117.77 113.10 4.67 0.50 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1FC8 'double helix' 1FC8 'hairpin 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 A CFL 12 1_555 -0.396 -0.303 0.080 -4.075 -4.793 -1.939 1 A_G1:CFL12_A A 1 ? A 12 ? 19 1 1 A G 2 1_555 A CFL 11 1_555 -1.075 -0.507 -0.446 1.420 -9.232 3.196 2 A_G2:CFL11_A A 2 ? A 11 ? 19 1 1 A A 3 1_555 A TAF 10 1_555 -0.051 -0.320 -0.723 10.512 -2.561 3.408 3 A_A3:TAF10_A A 3 ? A 10 ? 20 1 1 A C 4 1_555 A GFL 9 1_555 0.717 -0.254 -0.343 14.008 0.533 3.096 4 A_C4:GFL9_A A 4 ? A 9 ? 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 A CFL 12 1_555 A G 2 1_555 A CFL 11 1_555 0.592 -1.230 3.480 4.064 -2.066 32.379 -1.797 -0.288 3.595 -3.683 -7.243 32.689 1 AA_G1G2:CFL11CFL12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A G 2 1_555 A CFL 11 1_555 A A 3 1_555 A TAF 10 1_555 0.764 -0.733 3.147 -0.796 8.650 36.849 -2.172 -1.275 2.891 13.456 1.239 37.824 2 AA_G2A3:TAF10CFL11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A A 3 1_555 A TAF 10 1_555 A C 4 1_555 A GFL 9 1_555 0.800 -1.741 3.546 -0.908 3.661 33.430 -3.638 -1.539 3.320 6.339 1.572 33.636 3 AA_A3C4:GFL9TAF10_AA A 3 ? A 10 ? A 4 ? A 9 ? #