data_103D # _entry.id 103D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 103D pdb_0000103d 10.2210/pdb103d/pdb WWPDB D_1000170007 ? ? # 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 1995-03-31 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 5 'Structure model' 1 4 2024-05-22 # _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 7 5 'Structure model' 'Data collection' # 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 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond # 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 103D _pdbx_database_status.recvd_initial_deposition_date 1994-12-16 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _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 'Chou, S.-H.' 1 'Zhu, L.' 2 'Reid, B.R.' 3 # _citation.id primary _citation.title 'The unusual structure of the human centromere (GGA)2 motif. Unpaired guanosine residues stacked between sheared G.A pairs.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 244 _citation.page_first 259 _citation.page_last 268 _citation.year 1994 _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 7966337 _citation.pdbx_database_id_DOI 10.1006/jmbi.1994.1727 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Chou, S.H.' 1 ? primary 'Zhu, L.' 2 ? primary 'Reid, B.R.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*GP*TP*GP*GP*AP*AP*TP*GP*GP*AP*AP*C)-3') ; _entity.formula_weight 3751.466 _entity.pdbx_number_of_molecules 2 _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 no _entity_poly.pdbx_seq_one_letter_code '(DG)(DT)(DG)(DG)(DA)(DA)(DT)(DG)(DG)(DA)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GTGGAATGGAAC _entity_poly.pdbx_strand_id A,B _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 DG n 1 2 DT n 1 3 DG n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DG n 1 9 DG n 1 10 DA n 1 11 DA n 1 12 DC 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' # 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 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # 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 DG 1 1 1 DG G A . n A 1 2 DT 2 2 2 DT T A . n A 1 3 DG 3 3 3 DG G 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 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 DA 11 11 11 DA A A . n A 1 12 DC 12 12 12 DC C A . n B 1 1 DG 1 13 13 DG G B . n B 1 2 DT 2 14 14 DT T B . n B 1 3 DG 3 15 15 DG G B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DG 8 20 20 DG G B . n B 1 9 DG 9 21 21 DG G B . n B 1 10 DA 10 22 22 DA A B . n B 1 11 DA 11 23 23 DA A B . n B 1 12 DC 12 24 24 DC C B . n # _software.name AMBER _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 103D _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 103D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 103D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 103D _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 # _struct.entry_id 103D _struct.title 'THE UNUSUAL STRUCTURE OF THE HUMAN CENTROMERE (GGA)2 MOTIF: UNPAIRED GUANOSINE RESIDUES STACKED BETWEEN SHEARED G(DOT)A PAIRS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 103D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, DOUBLE HELIX, G-G STACKING, G:A MISMATCH, HUMAN CENTROMERE REPEAT, GA-BRACKETED G-STACK MOTIF' # 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 1 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 103D _struct_ref.pdbx_db_accession 103D _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 103D A 1 ? 12 ? 103D 1 ? 12 ? 1 12 2 1 103D B 1 ? 12 ? 103D 13 ? 24 ? 13 24 # _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 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DA 11 N1 ? ? A DG 1 B DA 23 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DA 11 N6 ? ? A DG 1 B DA 23 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog3 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 2 O2 ? ? ? 1_555 B DA 10 N6 ? ? A DT 2 B DA 22 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog7 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 11 N1 ? ? A DT 2 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 11 N6 ? ? A DT 2 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DA 10 N7 ? ? A DG 3 B DA 22 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A DG 3 N3 ? ? ? 1_555 B DA 10 N6 ? ? A DG 3 B DA 22 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 7 O2 ? ? A DA 5 B DT 19 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DG 8 N3 ? ? A DA 5 B DG 20 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog13 hydrog ? ? A DA 5 N7 ? ? ? 1_555 B DG 8 N2 ? ? A DA 5 B DG 20 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog14 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 O2 ? ? ? 1_555 B DA 5 N6 ? ? A DT 7 B DA 17 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DA 5 N7 ? ? A DG 8 B DA 17 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog20 hydrog ? ? A DG 8 N3 ? ? ? 1_555 B DA 5 N6 ? ? A DG 8 B DA 17 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog21 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 2 O2 ? ? A DA 10 B DT 14 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog22 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DG 3 N3 ? ? A DA 10 B DG 15 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog23 hydrog ? ? A DA 10 N7 ? ? ? 1_555 B DG 3 N2 ? ? A DA 10 B DG 15 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog24 hydrog ? ? A DA 11 N1 ? ? ? 1_555 B DG 1 N1 ? ? A DA 11 B DG 13 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog25 hydrog ? ? A DA 11 N6 ? ? ? 1_555 B DG 1 O6 ? ? A DA 11 B DG 13 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog26 hydrog ? ? A DA 11 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 11 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DA 11 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 11 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 110.21 108.30 1.91 0.30 N 2 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 111.39 108.30 3.09 0.30 N 3 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 110.48 108.30 2.18 0.30 N 4 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 110.81 108.30 2.51 0.30 N 5 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 111.00 108.30 2.70 0.30 N 6 1 "O4'" A DA 11 ? ? "C1'" A DA 11 ? ? N9 A DA 11 ? ? 110.33 108.30 2.03 0.30 N 7 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 110.78 108.30 2.48 0.30 N 8 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 110.18 108.30 1.88 0.30 N 9 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 110.13 108.30 1.83 0.30 N 10 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 111.37 108.30 3.07 0.30 N 11 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? N9 B DA 18 ? ? 110.56 108.30 2.26 0.30 N 12 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 110.79 108.30 2.49 0.30 N 13 1 "O4'" B DA 22 ? ? "C1'" B DA 22 ? ? N9 B DA 22 ? ? 111.02 108.30 2.72 0.30 N 14 1 "O4'" B DA 23 ? ? "C1'" B DA 23 ? ? N9 B DA 23 ? ? 110.20 108.30 1.90 0.30 N 15 1 "O4'" B DC 24 ? ? "C1'" B DC 24 ? ? N1 B DC 24 ? ? 110.71 108.30 2.41 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 DT A 2 ? ? 0.060 'SIDE CHAIN' 2 1 DT B 14 ? ? 0.060 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 103D _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_refine.entry_id 103D _pdbx_nmr_refine.method ? _pdbx_nmr_refine.details ;R VALUE 0.250 FINAL RMS COORD. SHIFT 0.65 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 772 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0. THE DUPLEX CONTAINS UNPAIRED STAGGERED GUANOSINE RESIDUES, WHICH CO-STACK BY INTERCALATION BETWEEN SHEARED G(DOT)A AND A(DOT)G BASE-PAIRS TO FORM AN INTERESTING NEW STRUCTURAL MOTIF, THE GA-BRACKETED G-STACK. THE TGGAA REPEAT UNIT CONTAINS SIX "STEPS", FOUR OF WHICH ARE NOT WATSON-CRICK BASE-PAIRS. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_software.name Discover _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors 'BIOSYM TECHNOLOGIES, INC.' _pdbx_nmr_software.ordinal 1 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 103D 'double helix' 103D 'mismatched base pair' 103D '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 DG 1 1_555 B DC 12 1_555 -0.698 -0.295 0.667 -7.334 8.154 0.964 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DT 2 1_555 B DA 11 1_555 0.276 -0.133 0.438 9.532 8.232 0.790 2 A_DT2:DA23_B A 2 ? B 23 ? 20 1 1 A DG 3 1_555 B DA 10 1_555 6.401 -4.264 1.175 27.084 -15.358 8.790 3 A_DG3:DA22_B A 3 ? B 22 ? 11 9 1 A DA 5 1_555 B DG 8 1_555 -6.364 -4.238 1.211 -29.347 -14.928 10.022 4 A_DA5:DG20_B A 5 ? B 20 ? 11 9 1 A DA 6 1_555 B DT 7 1_555 -0.225 -0.110 0.424 -10.770 10.139 0.687 5 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 0.218 -0.108 0.422 11.216 10.159 0.730 6 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DG 8 1_555 B DA 5 1_555 6.363 -4.240 1.212 29.274 -15.268 10.065 7 A_DG8:DA17_B A 8 ? B 17 ? 11 9 1 A DA 10 1_555 B DG 3 1_555 -6.396 -4.257 1.180 -27.086 -15.353 9.020 8 A_DA10:DG15_B A 10 ? B 15 ? 11 9 1 A DA 11 1_555 B DT 2 1_555 -0.277 -0.136 0.448 -9.672 8.457 0.906 9 A_DA11:DT14_B A 11 ? B 14 ? 20 1 1 A DC 12 1_555 B DG 1 1_555 0.701 -0.300 0.672 7.360 8.691 1.155 10 A_DC12:DG13_B A 12 ? B 13 ? 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 DG 1 1_555 B DC 12 1_555 A DT 2 1_555 B DA 11 1_555 -0.042 -0.639 2.955 3.390 -0.207 35.187 -1.025 0.521 2.942 -0.341 -5.591 35.345 1 AA_DG1DT2:DA23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DT 2 1_555 B DA 11 1_555 A DG 3 1_555 B DA 10 1_555 0.270 1.321 2.930 2.693 4.658 58.657 1.125 -0.149 3.027 4.744 -2.743 58.882 2 AA_DT2DG3:DA22DA23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DA 5 1_555 B DG 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.377 1.185 2.934 -3.372 5.833 58.976 0.927 0.225 3.044 5.903 3.413 59.325 3 AA_DA5DA6:DT19DG20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.004 -0.456 2.900 -0.083 2.341 32.747 -1.160 -0.020 2.862 4.145 0.147 32.828 4 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DG 8 1_555 B DA 5 1_555 0.365 1.170 2.944 3.381 6.033 58.793 0.902 -0.212 3.055 6.122 -3.431 59.162 5 AA_DT7DG8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DA 10 1_555 B DG 3 1_555 A DA 11 1_555 B DT 2 1_555 -0.257 1.293 2.928 -2.819 4.846 58.353 1.091 0.128 3.026 4.958 2.884 58.598 6 AA_DA10DA11:DT14DG15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DA 11 1_555 B DT 2 1_555 A DC 12 1_555 B DG 1 1_555 0.047 -0.669 2.953 -3.300 -0.058 34.960 -1.101 -0.523 2.937 -0.096 5.478 35.111 7 AA_DA11DC12:DG13DT14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 103D _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_