data_229D # _entry.id 229D # _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 229D pdb_0000229d 10.2210/pdb229d/pdb WWPDB D_1000177608 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 229D _pdbx_database_status.recvd_initial_deposition_date 1995-08-16 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr REL _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 'Basti, M.M.' 1 'Stuart, J.W.' 2 'Lam, A.T.' 3 'Guenther, R.' 4 'Agris, P.F.' 5 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Design, biological activity and NMR-solution structure of a DNA analogue of yeast tRNA(Phe) anticodon domain.' Nat.Struct.Biol. 3 38 44 1996 NSBIEW US 1072-8368 2024 ? 8548453 10.1038/nsb0196-38 1 ;Direct Observation of Two Base-Pairing Modes of a Cytosine-Thymine Analogue with Guanine in a DNA Z-Form Duplex: Significance for Base Analogue Mutagenesis ; J.Mol.Biol. 251 665 ? 1995 JMOBAK UK 0022-2836 0070 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Basti, M.M.' 1 ? primary 'Stuart, J.W.' 2 ? primary 'Lam, A.T.' 3 ? primary 'Guenther, R.' 4 ? primary 'Agris, P.F.' 5 ? 1 'Moore, M.H.' 6 ? 1 'Van Meervelt, L.' 7 ? 1 'Salisbury, S.A.' 8 ? 1 'Lin, P.K.T.' 9 ? 1 'Brown, D.M.' 10 ? # _cell.entry_id 229D _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 229D _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 ;DNA (5'-D(*CP*CP*AP*GP*AP*CP*(UMP)P*GP*AP*AP*(MG1)P*AP*(UMP)P*(5CM)P*(UMP)P*GP*G)-3') ; _entity.formula_weight 5222.388 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_keywords.entity_id 1 _entity_keywords.text 'DEOXYRIBONUCLEIC ACID' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DA)(DG)(DA)(DC)(UMP)(DG)(DA)(DA)(MG1)(DA)(UMP)(5CM)(UMP)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAGACUGAAGAUCUGG _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 DC n 1 2 DC n 1 3 DA n 1 4 DG n 1 5 DA n 1 6 DC n 1 7 UMP n 1 8 DG n 1 9 DA n 1 10 DA n 1 11 MG1 n 1 12 DA n 1 13 UMP n 1 14 5CM n 1 15 UMP n 1 16 DG n 1 17 DG 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 'CHEMICALLY SYNTHESIZED' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 229D _struct_ref.pdbx_db_accession 229D _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 229D _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 17 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 229D _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 17 _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 17 # 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 MG1 'DNA linking' n ;2'-DEOXY-1-METHYLGUANOSINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C11 H16 N5 O7 P' 361.248 UMP non-polymer . ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; DUMP 'C9 H13 N2 O8 P' 308.182 # _pdbx_nmr_refine.entry_id 229D _pdbx_nmr_refine.method ? _pdbx_nmr_refine.details ;NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 537 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE SOLUTION STRUCTURE OF THE 17-MER DNA HAIRPIN LOOP WAS DETERMINED BASED ON 246 DISTANCE AND DIHEDRAL RESTRAINTS ESTIMATED FROM 2D NOE SPECTRUM. TEN LOW ENERGY STRUCTURES WERE USED TO GENERATE THIS AVERAGE STRUCTURE WHICH WAS FURTHER ENERGY MINIMIZED. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 229D _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? _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_software.name Discover _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors 'BIOSYM TECHNOLOGIES' _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 229D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 229D _struct.title 'DNA ANALOG OF YEAST TRANSFER RNA PHE ANTICODON DOMAIN WITH MODIFIED BASES 5-METHYL CYTOSINE AND 1-METHYL GUANINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 229D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, TRANSFER RNA, ANTICODON, HAIRPIN LOOP' # _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 DC 6 "O3'" ? ? ? 1_555 A UMP 7 P ? ? A DC 6 A UMP 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale both ? A UMP 7 "O3'" ? ? ? 1_555 A DG 8 P ? ? A UMP 7 A DG 8 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale3 covale both ? A DA 10 "O3'" ? ? ? 1_555 A MG1 11 P ? ? A DA 10 A MG1 11 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale4 covale both ? A MG1 11 "O3'" ? ? ? 1_555 A DA 12 P ? ? A MG1 11 A DA 12 1_555 ? ? ? ? ? ? ? 1.622 ? ? covale5 covale both ? A DA 12 "O3'" ? ? ? 1_555 A UMP 13 P ? ? A DA 12 A UMP 13 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale6 covale both ? A UMP 13 "O3'" ? ? ? 1_555 A 5CM 14 P ? ? A UMP 13 A 5CM 14 1_555 ? ? ? ? ? ? ? 1.622 ? ? covale7 covale both ? A 5CM 14 "O3'" ? ? ? 1_555 A UMP 15 P ? ? A 5CM 14 A UMP 15 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale8 covale both ? A UMP 15 "O3'" ? ? ? 1_555 A DG 16 P ? ? A UMP 15 A DG 16 1_555 ? ? ? ? ? ? ? 1.623 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 17 N1 ? ? A DC 1 A DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 17 O6 ? ? A DC 1 A DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 17 N2 ? ? A DC 1 A DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 16 N1 ? ? A DC 2 A DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 16 O6 ? ? A DC 2 A DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 16 N2 ? ? A DC 2 A DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A UMP 15 N3 ? ? A DA 3 A UMP 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A UMP 15 O4 ? ? A DA 3 A UMP 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A 5CM 14 N3 ? ? A DG 4 A 5CM 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A 5CM 14 O2 ? ? A DG 4 A 5CM 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A 5CM 14 N4 ? ? A DG 4 A 5CM 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A UMP 13 N3 ? ? A DA 5 A UMP 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A UMP 13 O4 ? ? A DA 5 A UMP 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 229D _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 229D _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 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 UMP 7 7 7 UMP UMP A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DA 9 9 9 DA A A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 MG1 11 11 11 MG1 +G A . n A 1 12 DA 12 12 12 DA A A . n A 1 13 UMP 13 13 13 UMP UMP A . n A 1 14 5CM 14 14 14 5CM +C A . n A 1 15 UMP 15 15 15 UMP UMP A . n A 1 16 DG 16 16 16 DG G A . n A 1 17 DG 17 17 17 DG G 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 UMP 7 A UMP 7 ? U ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; 2 A MG1 11 A MG1 11 ? DG ? 3 A UMP 13 A UMP 13 ? U ;2'-DEOXYURIDINE 5'-MONOPHOSPHATE ; 4 A 5CM 14 A 5CM 14 ? DC ? 5 A UMP 15 A UMP 15 ? U ;2'-DEOXYURIDINE 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 1995-12-07 2 'Structure model' 1 1 2008-03-24 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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other # 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_database_status 3 4 'Structure model' pdbx_nmr_software 4 4 'Structure model' pdbx_struct_assembly 5 4 'Structure model' pdbx_struct_oper_list 6 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' '_pdbx_database_status.process_site' 4 4 'Structure model' '_pdbx_nmr_software.name' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 "C1'" A DC 2 ? ? "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? 103.45 110.10 -6.65 1.00 N 2 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 128.19 108.30 19.89 0.30 N 3 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 114.99 108.30 6.69 0.30 N 4 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 114.45 108.30 6.15 0.30 N 5 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 115.52 108.30 7.22 0.30 N 6 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? "C2'" A DG 8 ? ? 109.93 106.80 3.13 0.50 N 7 1 "O4'" A DA 9 ? ? "C1'" A DA 9 ? ? "C2'" A DA 9 ? ? 111.30 106.80 4.50 0.50 N 8 1 N9 A DA 9 ? ? "C1'" A DA 9 ? ? "C2'" A DA 9 ? ? 139.49 114.30 25.19 1.40 N 9 1 N9 A DA 9 ? ? C4 A DA 9 ? ? C5 A DA 9 ? ? 108.42 105.80 2.62 0.40 N 10 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 112.51 108.30 4.21 0.30 N 11 1 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 112.74 108.30 4.44 0.30 N 12 1 "O4'" A DG 16 ? ? "C1'" A DG 16 ? ? N9 A DG 16 ? ? 115.57 108.30 7.27 0.30 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 DC A 2 ? ? 0.116 'SIDE CHAIN' 2 1 DA A 3 ? ? 0.098 'SIDE CHAIN' 3 1 DG A 4 ? ? 0.054 'SIDE CHAIN' 4 1 DA A 5 ? ? 0.103 'SIDE CHAIN' 5 1 DC A 6 ? ? 0.220 'SIDE CHAIN' 6 1 DG A 8 ? ? 0.084 'SIDE CHAIN' 7 1 DA A 10 ? ? 0.148 'SIDE CHAIN' 8 1 DA A 12 ? ? 0.084 'SIDE CHAIN' 9 1 DG A 16 ? ? 0.065 'SIDE CHAIN' # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 "C1'" ? A DC 2 ? 'WRONG HAND' . 2 1 "C1'" ? A DA 9 ? PLANAR . 3 1 "C4'" ? A DG 17 ? 'WRONG HAND' . # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 229D 'double helix' 229D '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 DC 1 1_555 A DG 17 1_555 0.004 -0.068 -0.076 14.398 -14.793 -7.924 1 A_DC1:DG17_A A 1 ? A 17 ? 19 1 1 A DC 2 1_555 A DG 16 1_555 0.039 0.054 -0.547 18.016 1.521 -0.548 2 A_DC2:DG16_A A 2 ? A 16 ? 19 1 1 A DA 3 1_555 A UMP 15 1_555 0.289 0.137 0.454 34.759 -20.150 6.461 3 A_DA3:UMP15_A A 3 ? A 15 ? 20 1 1 A DG 4 1_555 A 5CM 14 1_555 -0.208 0.003 0.281 10.130 4.963 -3.855 4 A_DG4:5CM14_A A 4 ? A 14 ? 19 1 1 A DA 5 1_555 A UMP 13 1_555 -0.081 0.015 -0.102 8.086 12.530 -3.030 5 A_DA5:UMP13_A A 5 ? A 13 ? 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 DC 1 1_555 A DG 17 1_555 A DC 2 1_555 A DG 16 1_555 -2.014 0.667 3.245 7.125 18.199 3.177 -6.477 9.151 0.412 75.293 -29.476 19.798 1 AA_DC1DC2:DG16DG17_AA A 1 ? A 17 ? A 2 ? A 16 ? 1 A DC 2 1_555 A DG 16 1_555 A DA 3 1_555 A UMP 15 1_555 0.453 2.402 2.857 0.728 9.128 23.590 2.799 -0.821 3.536 21.327 -1.701 25.281 2 AA_DC2DA3:UMP15DG16_AA A 2 ? A 16 ? A 3 ? A 15 ? 1 A DA 3 1_555 A UMP 15 1_555 A DG 4 1_555 A 5CM 14 1_555 0.477 -0.720 4.076 2.570 14.441 24.696 -5.368 -0.268 3.206 30.562 -5.439 28.665 3 AA_DA3DG4:5CM14UMP15_AA A 3 ? A 15 ? A 4 ? A 14 ? 1 A DG 4 1_555 A 5CM 14 1_555 A DA 5 1_555 A UMP 13 1_555 0.296 0.222 3.729 3.103 18.584 26.400 -3.466 0.114 3.211 35.509 -5.930 32.337 4 AA_DG4DA5:UMP135CM14_AA A 4 ? A 14 ? A 5 ? A 13 ? #