data_1GJ1 # _entry.id 1GJ1 # _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 1GJ1 pdb_00001gj1 10.2210/pdb1gj1/pdb RCSB RCSB017370 ? ? WWPDB D_1000017370 ? ? # 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 2003-01-07 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 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_struct_assembly 3 4 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site 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' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1GJ1 _pdbx_database_status.recvd_initial_deposition_date 2002-10-14 _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_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1N0O 'ensemble model OF PDB ENTRY 1N0K' unspecified PDB 1N0K 'MINIMIZED AVERAGE STRUCTURE OF PDB ENTRY 1N0O' unspecified PDB 1G5K 'ENSEMBLE: 1G5K is the structure of the oligonucleotide containing the phosphoglycolate lesion without the bleomycin bound.' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Junker, H.-D.' 1 'Hoehn, S.T.' 2 'Bunt, R.C.' 3 'Marathius, V.' 4 'Chen, J.' 5 'Turner, C.J.' 6 'Stubbe, J.' 7 # _citation.id primary _citation.title ;Synthesis, Characterization and Solution Structure of Tethered Oligonucleotides Containing an Internal 3'-Phosphoglycolate, 5'-Phosphate Gapped Lesion ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 30 _citation.page_first 5497 _citation.page_last 5508 _citation.year 2002 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12490718 _citation.pdbx_database_id_DOI 10.1093/nar/gkf681 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Junker, H.-D.' 1 ? primary 'Hoehn, S.T.' 2 ? primary 'Bunt, R.C.' 3 ? primary 'Marathius, V.' 4 ? primary 'Chen, J.' 5 ? primary 'Turner, C.J.' 6 ? primary 'Stubbe, J.' 7 ? # 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'-D(*CP*CP*AP*AP*AP*G)-3'" 1802.232 1 ? ? ? ? 2 polymer syn "5'-D(P*AP*CP*TP*GP*GP*G)-3'" 1849.241 1 ? ? ? ? 3 polymer syn "5'-D(*CP*CP*CP*AP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'" 3942.572 1 ? ? ? ? 4 non-polymer man '2-PHOSPHOGLYCOLIC ACID' 156.031 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 polydeoxyribonucleotide no no '(DC)(DC)(DA)(DA)(DA)(DG)' CCAAAG A ? 2 polydeoxyribonucleotide no no '(DA)(DC)(DT)(DG)(DG)(DG)' ACTGGG B ? 3 polydeoxyribonucleotide no no '(DC)(DC)(DC)(DA)(DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DG)' CCCAGTACTTTGG C ? # _pdbx_entity_nonpoly.entity_id 4 _pdbx_entity_nonpoly.name '2-PHOSPHOGLYCOLIC ACID' _pdbx_entity_nonpoly.comp_id PGA # 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 DA n 1 5 DA n 1 6 DG n 2 1 DA n 2 2 DC n 2 3 DT n 2 4 DG n 2 5 DG n 2 6 DG n 3 1 DC n 3 2 DC n 3 3 DC n 3 4 DA n 3 5 DG n 3 6 DT n 3 7 DA n 3 8 DC n 3 9 DT n 3 10 DT n 3 11 DT n 3 12 DG n 3 13 DG n # 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 PGA non-polymer . '2-PHOSPHOGLYCOLIC ACID' ? 'C2 H5 O6 P' 156.031 # 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 DA 4 4 4 DA A A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DG 6 6 6 DG G A . n B 2 1 DA 1 8 7 DA T B . n B 2 2 DC 2 9 9 DC C B . n B 2 3 DT 3 10 10 DT T B . n B 2 4 DG 4 11 11 DG G B . n B 2 5 DG 5 12 12 DG G B . n B 2 6 DG 6 13 13 DG G B . n C 3 1 DC 1 14 14 DC C C . n C 3 2 DC 2 15 15 DC C C . n C 3 3 DC 3 16 16 DC C C . n C 3 4 DA 4 17 17 DA A C . n C 3 5 DG 5 18 18 DG G C . n C 3 6 DT 6 19 19 DT T C . n C 3 7 DA 7 20 20 DA A C . n C 3 8 DC 8 21 21 DC C C . n C 3 9 DT 9 22 22 DT T C . n C 3 10 DT 10 23 23 DT T C . n C 3 11 DT 11 24 24 DT T C . n C 3 12 DG 12 25 25 DG G C . n C 3 13 DG 13 26 26 DG G C . n # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id PGA _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 7 _pdbx_nonpoly_scheme.auth_seq_num 7 _pdbx_nonpoly_scheme.pdb_mon_id PGA _pdbx_nonpoly_scheme.auth_mon_id T _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _exptl.entry_id 1GJ1 _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 # _database_PDB_matrix.entry_id 1GJ1 _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 1GJ1 _struct.title ;NMR structure of d(CCAAAGXACTGGG), X is a 3'phosphoglycolate, 5'phosphate gapped lesion ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1GJ1 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, bleomycin, phosphoglycolate' # 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 ? C N N 3 ? D N N 4 ? # 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 1GJ1 1GJ1 ? ? ? 2 2 PDB 1GJ1 1GJ1 ? ? ? 3 3 PDB 1GJ1 1GJ1 ? ? ? # 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 1GJ1 A 1 ? 6 ? 1GJ1 1 ? 6 ? 1 6 2 2 1GJ1 B 1 ? 6 ? 1GJ1 8 ? 13 ? 8 13 3 3 1GJ1 C 1 ? 13 ? 1GJ1 14 ? 26 ? 14 26 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _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 # 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 one ? A DG 6 "O3'" ? ? ? 1_555 D PGA . P ? ? A DG 6 A PGA 7 1_555 ? ? ? ? ? ? ? 1.584 ? ? hydrog1 hydrog ? ? A DC 1 N4 ? ? ? 1_555 C DG 12 O6 ? ? A DC 1 C DG 25 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DC 1 N3 ? ? ? 1_555 C DG 13 N1 ? ? A DC 1 C DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 N4 ? ? ? 1_555 C DG 13 O6 ? ? A DC 1 C DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 1 O2 ? ? ? 1_555 C DG 13 N2 ? ? A DC 1 C DG 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N3 ? ? ? 1_555 C DG 12 N1 ? ? A DC 2 C DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DG 12 O6 ? ? A DC 2 C DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 2 O2 ? ? ? 1_555 C DG 12 N2 ? ? A DC 2 C DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N1 ? ? ? 1_555 C DT 11 N3 ? ? A DA 3 C DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 3 N6 ? ? ? 1_555 C DT 11 O4 ? ? A DA 3 C DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 C DT 9 O4 ? ? A DA 4 C DT 22 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog11 hydrog ? ? A DA 4 N1 ? ? ? 1_555 C DT 10 N3 ? ? A DA 4 C DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 4 N6 ? ? ? 1_555 C DT 10 O4 ? ? A DA 4 C DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 C DT 9 N3 ? ? A DA 5 C DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 C DT 9 O4 ? ? A DA 5 C DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N1 ? ? ? 1_555 C DC 8 N3 ? ? A DG 6 C DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N2 ? ? ? 1_555 C DC 8 O2 ? ? A DG 6 C DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 O6 ? ? ? 1_555 C DC 8 N4 ? ? A DG 6 C DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B DA 1 N1 ? ? ? 1_555 C DT 6 N3 ? ? B DA 8 C DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? B DA 1 N6 ? ? ? 1_555 C DT 6 O4 ? ? B DA 8 C DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B DC 2 N3 ? ? ? 1_555 C DG 5 N1 ? ? B DC 9 C DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B DC 2 N4 ? ? ? 1_555 C DG 5 O6 ? ? B DC 9 C DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B DC 2 O2 ? ? ? 1_555 C DG 5 N2 ? ? B DC 9 C DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B DT 3 N3 ? ? ? 1_555 C DA 4 N1 ? ? B DT 10 C DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B DT 3 O4 ? ? ? 1_555 C DA 4 N6 ? ? B DT 10 C DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B DG 4 O6 ? ? ? 1_555 C DC 2 N4 ? ? B DG 11 C DC 15 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog26 hydrog ? ? B DG 4 N1 ? ? ? 1_555 C DC 3 N3 ? ? B DG 11 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B DG 4 N2 ? ? ? 1_555 C DC 3 O2 ? ? B DG 11 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DG 4 O6 ? ? ? 1_555 C DC 3 N4 ? ? B DG 11 C DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DG 5 O6 ? ? ? 1_555 C DC 1 N4 ? ? B DG 12 C DC 14 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog30 hydrog ? ? B DG 5 N1 ? ? ? 1_555 C DC 2 N3 ? ? B DG 12 C DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B DG 5 N2 ? ? ? 1_555 C DC 2 O2 ? ? B DG 12 C DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B DG 5 O6 ? ? ? 1_555 C DC 2 N4 ? ? B DG 12 C DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B DG 6 N1 ? ? ? 1_555 C DC 1 N3 ? ? B DG 13 C DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B DG 6 N2 ? ? ? 1_555 C DC 1 O2 ? ? B DG 13 C DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B DG 6 O6 ? ? ? 1_555 C DC 1 N4 ? ? B DG 13 C DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id PGA _struct_site.pdbx_auth_seq_id 7 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 1 _struct_site.details 'BINDING SITE FOR RESIDUE PGA A 7' # _struct_site_gen.id 1 _struct_site_gen.site_id AC1 _struct_site_gen.pdbx_num_res 1 _struct_site_gen.label_comp_id DG _struct_site_gen.label_asym_id A _struct_site_gen.label_seq_id 6 _struct_site_gen.pdbx_auth_ins_code ? _struct_site_gen.auth_comp_id DG _struct_site_gen.auth_asym_id A _struct_site_gen.auth_seq_id 6 _struct_site_gen.label_atom_id . _struct_site_gen.label_alt_id ? _struct_site_gen.symmetry 1_555 _struct_site_gen.details ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P B DA 8 ? ? OP3 B DA 8 ? ? 1.479 1.607 -0.128 0.012 N 2 1 N1 B DT 10 ? ? C2 B DT 10 ? ? 1.430 1.376 0.054 0.008 N 3 1 "C5'" B DG 11 ? ? "C4'" B DG 11 ? ? 1.554 1.512 0.042 0.007 N 4 1 N1 C DT 19 ? ? C2 C DT 19 ? ? 1.429 1.376 0.053 0.008 N 5 1 "C5'" C DT 23 ? ? "C4'" C DT 23 ? ? 1.558 1.512 0.046 0.007 N 6 1 "C5'" C DT 24 ? ? "C4'" C DT 24 ? ? 1.561 1.512 0.049 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 97.40 102.40 -5.00 0.80 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.00 108.30 3.70 0.30 N 3 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 122.87 118.90 3.97 0.60 N 4 1 "C3'" A DC 2 ? ? "O3'" A DC 2 ? ? P A DA 3 ? ? 127.57 119.70 7.87 1.20 Y 5 1 N1 A DA 3 ? ? C6 A DA 3 ? ? N6 A DA 3 ? ? 123.62 118.60 5.02 0.60 N 6 1 "C3'" A DA 3 ? ? "O3'" A DA 3 ? ? P A DA 4 ? ? 129.35 119.70 9.65 1.20 Y 7 1 N1 A DA 5 ? ? C6 A DA 5 ? ? N6 A DA 5 ? ? 123.31 118.60 4.71 0.60 N 8 1 N1 B DA 8 ? ? C6 B DA 8 ? ? N6 B DA 8 ? ? 122.87 118.60 4.27 0.60 N 9 1 N1 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 122.74 118.90 3.84 0.60 N 10 1 "C3'" B DT 10 ? ? "O3'" B DT 10 ? ? P B DG 11 ? ? 130.61 119.70 10.91 1.20 Y 11 1 N3 B DG 11 ? ? C2 B DG 11 ? ? N2 B DG 11 ? ? 126.36 119.90 6.46 0.70 N 12 1 N3 B DG 12 ? ? C2 B DG 12 ? ? N2 B DG 12 ? ? 124.86 119.90 4.96 0.70 N 13 1 N3 B DG 13 ? ? C2 B DG 13 ? ? N2 B DG 13 ? ? 125.23 119.90 5.33 0.70 N 14 1 "O4'" C DC 14 ? ? "C1'" C DC 14 ? ? N1 C DC 14 ? ? 110.20 108.30 1.90 0.30 N 15 1 N1 C DC 16 ? ? C2 C DC 16 ? ? O2 C DC 16 ? ? 122.56 118.90 3.66 0.60 N 16 1 "C3'" C DC 16 ? ? "O3'" C DC 16 ? ? P C DA 17 ? ? 127.87 119.70 8.17 1.20 Y 17 1 "C3'" C DA 17 ? ? "O3'" C DA 17 ? ? P C DG 18 ? ? 127.30 119.70 7.60 1.20 Y 18 1 N3 C DG 18 ? ? C2 C DG 18 ? ? N2 C DG 18 ? ? 124.82 119.90 4.92 0.70 N 19 1 "O4'" C DT 19 ? ? "C1'" C DT 19 ? ? "C2'" C DT 19 ? ? 101.04 105.90 -4.86 0.80 N 20 1 "C3'" C DT 19 ? ? "O3'" C DT 19 ? ? P C DA 20 ? ? 128.77 119.70 9.07 1.20 Y 21 1 "O4'" C DT 22 ? ? "C1'" C DT 22 ? ? N1 C DT 22 ? ? 110.19 108.30 1.89 0.30 N 22 1 C4 C DT 23 ? ? C5 C DT 23 ? ? C7 C DT 23 ? ? 122.61 119.00 3.61 0.60 N 23 1 C6 C DT 23 ? ? C5 C DT 23 ? ? C7 C DT 23 ? ? 118.18 122.90 -4.72 0.60 N 24 1 N3 C DG 25 ? ? C2 C DG 25 ? ? N2 C DG 25 ? ? 124.99 119.90 5.09 0.70 N 25 1 "C3'" C DG 25 ? ? "O3'" C DG 25 ? ? P C DG 26 ? ? 129.36 119.70 9.66 1.20 Y 26 1 N3 C DG 26 ? ? C2 C DG 26 ? ? N2 C DG 26 ? ? 125.28 119.90 5.38 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 DC A 2 ? ? 0.063 'SIDE CHAIN' 2 1 DA A 3 ? ? 0.056 'SIDE CHAIN' 3 1 DA A 4 ? ? 0.078 'SIDE CHAIN' 4 1 DC B 9 ? ? 0.078 'SIDE CHAIN' 5 1 DG B 11 ? ? 0.072 'SIDE CHAIN' 6 1 DG B 12 ? ? 0.126 'SIDE CHAIN' 7 1 DC C 15 ? ? 0.088 'SIDE CHAIN' 8 1 DC C 16 ? ? 0.061 'SIDE CHAIN' 9 1 DG C 18 ? ? 0.097 'SIDE CHAIN' 10 1 DT C 19 ? ? 0.077 'SIDE CHAIN' 11 1 DT C 22 ? ? 0.072 'SIDE CHAIN' 12 1 DT C 23 ? ? 0.101 'SIDE CHAIN' 13 1 DT C 24 ? ? 0.066 'SIDE CHAIN' 14 1 DG C 25 ? ? 0.059 'SIDE CHAIN' 15 1 DG C 26 ? ? 0.082 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 1GJ1 _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'MINIMUM RMSD AND NMR CONSTRAINTS VIOLATION' _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 1GJ1 _pdbx_nmr_representative.conformer_id ? _pdbx_nmr_representative.selection_criteria 'minimized average structure' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '1.4 mM oligonucleotide' _pdbx_nmr_sample_details.solvent_system ? # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293.15 _pdbx_nmr_exptl_sample_conditions.pressure 1.0 _pdbx_nmr_exptl_sample_conditions.pH 6.9 _pdbx_nmr_exptl_sample_conditions.ionic_strength '40 mM NaH2PO4' _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 PECOSY 2 1 1 TOCSY 3 1 1 NOESY 4 1 1 HSQC 5 1 1 GE-HSQC # _pdbx_nmr_refine.entry_id 1GJ1 _pdbx_nmr_refine.method 'CONJUGATE GRADIENT MINIMIZATION' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal X-PLOR 3.851 refinement Brunger 1 X-PLOR 3.851 'structure solution' Brunger 2 # 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 PGA P P N N 144 PGA O1P O N N 145 PGA O2P O N N 146 PGA O3P O N N 147 PGA O4P O N N 148 PGA C2 C N N 149 PGA C1 C N N 150 PGA O1 O N N 151 PGA O2 O N N 152 PGA HOP3 H N N 153 PGA HOP4 H N N 154 PGA H21 H N N 155 PGA H22 H N N 156 PGA HO2 H N N 157 # 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 PGA P O1P sing N N 150 PGA P O2P doub N N 151 PGA P O3P sing N N 152 PGA P O4P sing N N 153 PGA O1P C2 sing N N 154 PGA O3P HOP3 sing N N 155 PGA O4P HOP4 sing N N 156 PGA C2 C1 sing N N 157 PGA C2 H21 sing N N 158 PGA C2 H22 sing N N 159 PGA C1 O1 doub N N 160 PGA C1 O2 sing N N 161 PGA O2 HO2 sing N N 162 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1GJ1 'double helix' 1GJ1 'b-form double helix' 1GJ1 '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 DC 1 1_555 C DG 13 1_555 1.058 -0.626 1.121 -12.981 -19.944 -8.154 1 A_DC1:DG26_C A 1 ? C 26 ? 19 1 1 A DC 2 1_555 C DG 12 1_555 1.124 -0.501 0.798 -10.015 -2.055 -0.439 2 A_DC2:DG25_C A 2 ? C 25 ? 19 1 1 A DA 3 1_555 C DT 11 1_555 0.055 -0.178 0.721 24.587 -9.052 -10.790 3 A_DA3:DT24_C A 3 ? C 24 ? 20 1 1 A DA 4 1_555 C DT 10 1_555 -0.152 -0.232 0.433 19.026 -21.830 -4.253 4 A_DA4:DT23_C A 4 ? C 23 ? 20 1 1 A DA 5 1_555 C DT 9 1_555 0.036 -0.219 0.973 26.296 -11.795 -10.973 5 A_DA5:DT22_C A 5 ? C 22 ? 20 1 1 A DG 6 1_555 C DC 8 1_555 -0.585 -0.286 0.508 22.192 -13.697 -1.876 6 A_DG6:DC21_C A 6 ? C 21 ? 19 1 1 B DA 1 1_555 C DT 6 1_555 0.119 -0.113 0.203 -3.410 13.087 -8.475 7 B_DA8:DT19_C B 8 ? C 19 ? 20 1 1 B DC 2 1_555 C DG 5 1_555 0.940 -0.432 0.943 -17.631 -11.279 -4.883 8 B_DC9:DG18_C B 9 ? C 18 ? 19 1 1 B DT 3 1_555 C DA 4 1_555 0.123 -0.195 0.130 -6.458 -0.615 -6.721 9 B_DT10:DA17_C B 10 ? C 17 ? 20 1 1 B DG 4 1_555 C DC 3 1_555 -0.696 -0.480 1.089 17.247 -3.803 -8.743 10 B_DG11:DC16_C B 11 ? C 16 ? 19 1 1 B DG 5 1_555 C DC 2 1_555 -0.823 -0.497 1.154 22.981 -12.672 -5.615 11 B_DG12:DC15_C B 12 ? C 15 ? 19 1 1 B DG 6 1_555 C DC 1 1_555 -0.897 -0.579 1.002 4.256 -19.554 -7.743 12 B_DG13:DC14_C B 13 ? C 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 DC 1 1_555 C DG 13 1_555 A DC 2 1_555 C DG 12 1_555 0.527 -0.513 3.139 3.206 -4.338 42.941 -0.284 -0.410 3.203 -5.898 -4.359 43.263 1 AA_DC1DC2:DG25DG26_CC A 1 ? C 26 ? A 2 ? C 25 ? 1 A DC 2 1_555 C DG 12 1_555 A DA 3 1_555 C DT 11 1_555 -0.026 -0.744 2.324 2.564 -1.441 27.775 -1.297 0.490 2.347 -2.991 -5.322 27.927 2 AA_DC2DA3:DT24DG25_CC A 2 ? C 25 ? A 3 ? C 24 ? 1 A DA 3 1_555 C DT 11 1_555 A DA 4 1_555 C DT 10 1_555 -0.132 -0.539 3.426 -4.375 4.791 39.827 -1.343 -0.322 3.337 6.976 6.372 40.330 3 AA_DA3DA4:DT23DT24_CC A 3 ? C 24 ? A 4 ? C 23 ? 1 A DA 4 1_555 C DT 10 1_555 A DA 5 1_555 C DT 9 1_555 0.364 0.067 2.986 -5.141 -9.710 39.351 1.066 -1.035 2.825 -14.089 7.459 40.798 4 AA_DA4DA5:DT22DT23_CC A 4 ? C 23 ? A 5 ? C 22 ? 1 A DA 5 1_555 C DT 9 1_555 A DG 6 1_555 C DC 8 1_555 0.030 -0.471 3.291 3.454 1.815 38.097 -0.947 0.389 3.257 2.772 -5.274 38.289 5 AA_DA5DG6:DC21DT22_CC A 5 ? C 22 ? A 6 ? C 21 ? 1 A DG 6 1_555 C DC 8 1_555 B DA 1 1_555 C DT 6 1_555 0.416 0.400 7.068 -21.990 -14.751 82.340 1.019 -1.387 6.694 -10.956 16.333 85.765 6 AB_DG6DA8:DT19DC21_CC A 6 ? C 21 ? B 8 ? C 19 ? 1 B DA 1 1_555 C DT 6 1_555 B DC 2 1_555 C DG 5 1_555 -0.326 -0.518 4.750 1.237 -20.463 36.174 2.560 0.661 4.409 -30.164 -1.824 41.409 7 BB_DA8DC9:DG18DT19_CC B 8 ? C 19 ? B 9 ? C 18 ? 1 B DC 2 1_555 C DG 5 1_555 B DT 3 1_555 C DA 4 1_555 -0.023 -0.547 3.112 7.211 -1.516 35.368 -0.677 1.011 3.068 -2.463 -11.712 36.104 8 BB_DC9DT10:DA17DG18_CC B 9 ? C 18 ? B 10 ? C 17 ? 1 B DT 3 1_555 C DA 4 1_555 B DG 4 1_555 C DC 3 1_555 0.017 -1.043 2.656 -6.682 -4.967 33.004 -1.121 -0.921 2.725 -8.574 11.534 34.009 9 BB_DT10DG11:DC16DA17_CC B 10 ? C 17 ? B 11 ? C 16 ? 1 B DG 4 1_555 C DC 3 1_555 B DG 5 1_555 C DC 2 1_555 0.019 0.066 3.185 3.861 -7.270 40.069 0.872 0.385 3.116 -10.476 -5.564 40.872 10 BB_DG11DG12:DC15DC16_CC B 11 ? C 16 ? B 12 ? C 15 ? 1 B DG 5 1_555 C DC 2 1_555 B DG 6 1_555 C DC 1 1_555 0.260 0.147 3.556 -0.319 -2.039 44.768 0.394 -0.372 3.545 -2.676 0.419 44.814 11 BB_DG12DG13:DC14DC15_CC B 12 ? C 15 ? B 13 ? C 14 ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? ? 'custom build' 500 2 ? ? 'custom build' 600 3 ? ? 'custom build' 750 # _atom_sites.entry_id 1GJ1 _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_