data_5J05 # _entry.id 5J05 # _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 5J05 pdb_00005j05 10.2210/pdb5j05/pdb WWPDB D_1000218830 ? ? BMRB 30045 ? 10.13018/BMR30045 # 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 2017-04-05 2 'Structure model' 1 1 2018-10-10 3 'Structure model' 1 2 2019-05-08 4 'Structure model' 1 3 2019-10-23 5 'Structure model' 1 4 2024-05-15 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Data collection' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Experimental preparation' 7 5 'Structure model' 'Data collection' 8 5 'Structure model' 'Database references' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_seq_map_depositor_info 5 4 'Structure model' ndb_struct_na_base_pair 6 4 'Structure model' ndb_struct_na_base_pair_step 7 4 'Structure model' pdbx_nmr_exptl_sample_conditions 8 4 'Structure model' struct_conn 9 5 'Structure model' chem_comp_atom 10 5 'Structure model' chem_comp_bond 11 5 'Structure model' database_2 # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.journal_volume' 6 2 'Structure model' '_citation.page_first' 7 2 'Structure model' '_citation.page_last' 8 2 'Structure model' '_citation.pdbx_database_id_DOI' 9 2 'Structure model' '_citation.pdbx_database_id_PubMed' 10 2 'Structure model' '_citation.title' 11 2 'Structure model' '_citation.year' 12 2 'Structure model' '_citation_author.identifier_ORCID' 13 3 'Structure model' '_pdbx_nmr_software.name' 14 3 'Structure model' '_pdbx_seq_map_depositor_info.one_letter_code_mod' 15 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.temperature' 16 4 'Structure model' '_pdbx_nmr_exptl_sample_conditions.temperature_units' 17 5 'Structure model' '_database_2.pdbx_DOI' 18 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 5J05 _pdbx_database_status.recvd_initial_deposition_date 2016-03-27 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details . _pdbx_database_related.db_id 30045 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Dvorkin, S.A.' 1 'Karsisiotis, A.I.' 2 'Webba da Silva, M.' 3 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Sci Adv' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2375-2548 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 4 _citation.language ? _citation.page_first eaat3007 _citation.page_last eaat3007 _citation.title 'Encoding canonical DNA quadruplex structure.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1126/sciadv.aat3007 _citation.pdbx_database_id_PubMed 30182059 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dvorkin, S.A.' 1 0000-0003-2924-751X primary 'Karsisiotis, A.I.' 2 ? primary 'Webba da Silva, M.' 3 0000-0001-6146-2522 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*AP*GP*GP*G)-3') ; _entity.formula_weight 6348.070 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _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)(DG)(DG)(DT)(DT)(DT)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DG)(DG)(DG)(DA)(DG)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGGTTTGGGTTTTGGGAGGG _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 DG n 1 2 DG n 1 3 DG n 1 4 DT n 1 5 DT n 1 6 DT n 1 7 DG n 1 8 DG n 1 9 DG n 1 10 DT n 1 11 DT n 1 12 DT n 1 13 DT n 1 14 DG n 1 15 DG n 1 16 DG n 1 17 DA n 1 18 DG n 1 19 DG n 1 20 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 20 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 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 DG A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DT 4 4 4 DT DT A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DT 11 11 11 DT DT A . n A 1 12 DT 12 12 12 DT DT A . n A 1 13 DT 13 13 13 DT DT A . n A 1 14 DG 14 14 14 DG DG A . n A 1 15 DG 15 15 15 DG DG A . n A 1 16 DG 16 16 16 DG DG A . n A 1 17 DA 17 17 17 DA DA A . n A 1 18 DG 18 18 18 DG DG A . n A 1 19 DG 19 19 19 DG DG A . n A 1 20 DG 20 20 20 DG DG A . n # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 5J05 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 5J05 _struct.title 'DIY G-Quadruplexes: Solution structure of d(GGGTTTGGGTTTTGGGAGGG) in sodium' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5J05 _struct_keywords.text 'Quadruplex (-ld+l) topology, Structure from MOLMOL, DNA' _struct_keywords.pdbx_keywords DNA # _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_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 5J05 _struct_ref.pdbx_db_accession 5J05 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5J05 _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 20 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 5J05 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 20 _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 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 3160 ? # _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 ? _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_ _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 N7 ? ? ? 1_555 A DG 9 N2 ? ? A DG 1 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DG 9 N1 ? ? A DG 1 A DG 9 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DG 14 O6 ? ? A DG 1 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DG 14 N7 ? ? A DG 1 A DG 14 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DG 8 O6 ? ? A DG 2 A DG 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DG 8 N7 ? ? A DG 2 A DG 8 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 2 N7 ? ? ? 1_555 A DG 15 N2 ? ? A DG 2 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DG 15 N1 ? ? A DG 2 A DG 15 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DG 3 N7 ? ? ? 1_555 A DG 7 N2 ? ? A DG 3 A DG 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog10 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DG 7 N1 ? ? A DG 3 A DG 7 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog11 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DG 16 O6 ? ? A DG 3 A DG 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog12 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 16 N7 ? ? A DG 3 A DG 16 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog13 hydrog ? ? A DG 7 N7 ? ? ? 1_555 A DG 18 N2 ? ? A DG 7 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog14 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A DG 18 N1 ? ? A DG 7 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog15 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DG 19 O6 ? ? A DG 8 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog16 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DG 19 N7 ? ? A DG 8 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog17 hydrog ? ? A DG 9 N7 ? ? ? 1_555 A DG 20 N2 ? ? A DG 9 A DG 20 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog18 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DG 20 N1 ? ? A DG 9 A DG 20 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog19 hydrog ? ? A DT 10 N3 ? ? ? 1_555 A DT 13 O4 ? ? A DT 10 A DT 13 1_555 ? ? ? ? ? ? 'DT-DT MISPAIR' ? ? ? hydrog20 hydrog ? ? A DT 10 O4 ? ? ? 1_555 A DG 20 N2 ? ? A DT 10 A DG 20 1_555 ? ? ? ? ? ? 'DT-DG MISPAIR' ? ? ? hydrog21 hydrog ? ? A DT 11 N3 ? ? ? 1_555 A DT 13 O4 ? ? A DT 11 A DT 13 1_555 ? ? ? ? ? ? 'DT-DT MISPAIR' ? ? ? hydrog22 hydrog ? ? A DG 14 N1 ? ? ? 1_555 A DG 20 O6 ? ? A DG 14 A DG 20 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? A DG 14 N2 ? ? ? 1_555 A DG 20 N7 ? ? A DG 14 A DG 20 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? A DG 15 N7 ? ? ? 1_555 A DG 19 N2 ? ? A DG 15 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? A DG 15 O6 ? ? ? 1_555 A DG 19 N1 ? ? A DG 15 A DG 19 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? A DG 16 N1 ? ? ? 1_555 A DG 18 O6 ? ? A DG 16 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? A DG 16 N2 ? ? ? 1_555 A DG 18 N7 ? ? A DG 16 A DG 18 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _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 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.13 122.90 -3.77 0.60 N 2 1 C6 A DT 13 ? ? C5 A DT 13 ? ? C7 A DT 13 ? ? 119.26 122.90 -3.64 0.60 N 3 2 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.29 122.90 -3.61 0.60 N 4 2 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.28 108.30 1.98 0.30 N 5 3 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.78 108.30 2.48 0.30 N 6 3 "O4'" A DT 11 ? ? "C1'" A DT 11 ? ? N1 A DT 11 ? ? 110.23 108.30 1.93 0.30 N 7 4 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.28 122.90 -3.62 0.60 N 8 4 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.58 108.30 2.28 0.30 N 9 5 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.32 108.30 2.02 0.30 N 10 6 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.23 122.90 -3.67 0.60 N 11 6 "O4'" A DT 11 ? ? "C1'" A DT 11 ? ? N1 A DT 11 ? ? 110.48 108.30 2.18 0.30 N 12 7 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.41 108.30 2.11 0.30 N 13 8 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.04 122.90 -3.86 0.60 N 14 8 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.24 122.90 -3.66 0.60 N 15 8 "O4'" A DT 11 ? ? "C1'" A DT 11 ? ? N1 A DT 11 ? ? 111.38 108.30 3.08 0.30 N 16 9 "O4'" A DT 11 ? ? "C1'" A DT 11 ? ? N1 A DT 11 ? ? 110.22 108.30 1.92 0.30 N 17 10 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 119.01 122.90 -3.89 0.60 N 18 10 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.11 122.90 -3.79 0.60 N 19 10 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 110.27 108.30 1.97 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 DG A 16 ? ? 0.066 'SIDE CHAIN' 2 2 DG A 16 ? ? 0.057 'SIDE CHAIN' 3 3 DG A 1 ? ? 0.055 'SIDE CHAIN' 4 3 DG A 16 ? ? 0.073 'SIDE CHAIN' 5 4 DG A 16 ? ? 0.062 'SIDE CHAIN' 6 5 DG A 3 ? ? 0.055 'SIDE CHAIN' 7 5 DG A 16 ? ? 0.069 'SIDE CHAIN' 8 6 DG A 16 ? ? 0.054 'SIDE CHAIN' 9 7 DG A 3 ? ? 0.052 'SIDE CHAIN' 10 7 DG A 16 ? ? 0.058 'SIDE CHAIN' 11 8 DG A 16 ? ? 0.064 'SIDE CHAIN' 12 9 DG A 16 ? ? 0.058 'SIDE CHAIN' 13 10 DG A 16 ? ? 0.065 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 5J05 _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _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 5J05 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '1 mM DNA, 93% H2O/7% D2O' '93% H2O/7% D2O' 'S092 in H2O' solution '20 mM NaPi, pH 6.8' 2 '1 mM DNA, 100% D2O' '100% D2O' 'S092 in D2O' solution '20 mM NaPi, pH 6.8' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 DNA 1 ? mM none 2 DNA 1 ? mM none # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293.15 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength '20 mM NaPi' _pdbx_nmr_exptl_sample_conditions.details '20 mM NaPi, pH 6.8' _pdbx_nmr_exptl_sample_conditions.ionic_strength_err 0.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label 'S092 in H2O' _pdbx_nmr_exptl_sample_conditions.pH_err 0.2 _pdbx_nmr_exptl_sample_conditions.pH_units pD _pdbx_nmr_exptl_sample_conditions.pressure_err 0.2 _pdbx_nmr_exptl_sample_conditions.temperature_err 0.2 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 'H,H jr-NOESY' 1 isotropic 2 1 2 '2D 1H-1H NOESY' 1 isotropic # _pdbx_nmr_refine.entry_id 5J05 _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 2 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement Felix ? 'Accelrys Software Inc.' 2 'structure calculation' Xplor-NIH ? 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' Felix ? 'Accelrys Software Inc.' # 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 DG OP3 O N N 37 DG P P N N 38 DG OP1 O N N 39 DG OP2 O N N 40 DG "O5'" O N N 41 DG "C5'" C N N 42 DG "C4'" C N R 43 DG "O4'" O N N 44 DG "C3'" C N S 45 DG "O3'" O N N 46 DG "C2'" C N N 47 DG "C1'" C N R 48 DG N9 N Y N 49 DG C8 C Y N 50 DG N7 N Y N 51 DG C5 C Y N 52 DG C6 C N N 53 DG O6 O N N 54 DG N1 N N N 55 DG C2 C N N 56 DG N2 N N N 57 DG N3 N N N 58 DG C4 C Y N 59 DG HOP3 H N N 60 DG HOP2 H N N 61 DG "H5'" H N N 62 DG "H5''" H N N 63 DG "H4'" H N N 64 DG "H3'" H N N 65 DG "HO3'" H N N 66 DG "H2'" H N N 67 DG "H2''" H N N 68 DG "H1'" H N N 69 DG H8 H N N 70 DG H1 H N N 71 DG H21 H N N 72 DG H22 H N N 73 DT OP3 O N N 74 DT P P N N 75 DT OP1 O N N 76 DT OP2 O N N 77 DT "O5'" O N N 78 DT "C5'" C N N 79 DT "C4'" C N R 80 DT "O4'" O N N 81 DT "C3'" C N S 82 DT "O3'" O N N 83 DT "C2'" C N N 84 DT "C1'" C N R 85 DT N1 N N N 86 DT C2 C N N 87 DT O2 O N N 88 DT N3 N N N 89 DT C4 C N N 90 DT O4 O N N 91 DT C5 C N N 92 DT C7 C N N 93 DT C6 C N N 94 DT HOP3 H N N 95 DT HOP2 H N N 96 DT "H5'" H N N 97 DT "H5''" H N N 98 DT "H4'" H N N 99 DT "H3'" H N N 100 DT "HO3'" H N N 101 DT "H2'" H N N 102 DT "H2''" H N N 103 DT "H1'" H N N 104 DT H3 H N N 105 DT H71 H N N 106 DT H72 H N N 107 DT H73 H N N 108 DT H6 H N N 109 # 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 DG OP3 P sing N N 39 DG OP3 HOP3 sing N N 40 DG P OP1 doub N N 41 DG P OP2 sing N N 42 DG P "O5'" sing N N 43 DG OP2 HOP2 sing N N 44 DG "O5'" "C5'" sing N N 45 DG "C5'" "C4'" sing N N 46 DG "C5'" "H5'" sing N N 47 DG "C5'" "H5''" sing N N 48 DG "C4'" "O4'" sing N N 49 DG "C4'" "C3'" sing N N 50 DG "C4'" "H4'" sing N N 51 DG "O4'" "C1'" sing N N 52 DG "C3'" "O3'" sing N N 53 DG "C3'" "C2'" sing N N 54 DG "C3'" "H3'" sing N N 55 DG "O3'" "HO3'" sing N N 56 DG "C2'" "C1'" sing N N 57 DG "C2'" "H2'" sing N N 58 DG "C2'" "H2''" sing N N 59 DG "C1'" N9 sing N N 60 DG "C1'" "H1'" sing N N 61 DG N9 C8 sing Y N 62 DG N9 C4 sing Y N 63 DG C8 N7 doub Y N 64 DG C8 H8 sing N N 65 DG N7 C5 sing Y N 66 DG C5 C6 sing N N 67 DG C5 C4 doub Y N 68 DG C6 O6 doub N N 69 DG C6 N1 sing N N 70 DG N1 C2 sing N N 71 DG N1 H1 sing N N 72 DG C2 N2 sing N N 73 DG C2 N3 doub N N 74 DG N2 H21 sing N N 75 DG N2 H22 sing N N 76 DG N3 C4 sing N N 77 DT OP3 P sing N N 78 DT OP3 HOP3 sing N N 79 DT P OP1 doub N N 80 DT P OP2 sing N N 81 DT P "O5'" sing N N 82 DT OP2 HOP2 sing N N 83 DT "O5'" "C5'" sing N N 84 DT "C5'" "C4'" sing N N 85 DT "C5'" "H5'" sing N N 86 DT "C5'" "H5''" sing N N 87 DT "C4'" "O4'" sing N N 88 DT "C4'" "C3'" sing N N 89 DT "C4'" "H4'" sing N N 90 DT "O4'" "C1'" sing N N 91 DT "C3'" "O3'" sing N N 92 DT "C3'" "C2'" sing N N 93 DT "C3'" "H3'" sing N N 94 DT "O3'" "HO3'" sing N N 95 DT "C2'" "C1'" sing N N 96 DT "C2'" "H2'" sing N N 97 DT "C2'" "H2''" sing N N 98 DT "C1'" N1 sing N N 99 DT "C1'" "H1'" sing N N 100 DT N1 C2 sing N N 101 DT N1 C6 sing N N 102 DT C2 O2 doub N N 103 DT C2 N3 sing N N 104 DT N3 C4 sing N N 105 DT N3 H3 sing N N 106 DT C4 O4 doub N N 107 DT C4 C5 sing N N 108 DT C5 C7 sing N N 109 DT C5 C6 doub N N 110 DT C7 H71 sing N N 111 DT C7 H72 sing N N 112 DT C7 H73 sing N N 113 DT C6 H6 sing N N 114 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5J05 'double helix' 5J05 'quadruple 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 DT 11 1_555 A DT 13 1_555 2.939 2.395 -0.033 1.621 -36.446 -61.818 1 A_DT11:DT13_A A 11 ? A 13 ? ? ? 1 A DG 20 1_555 A DG 14 1_555 -0.409 -3.792 -0.075 -1.747 2.371 91.680 2 A_DG20:DG14_A A 20 ? A 14 ? 6 3 1 A DG 15 1_555 A DG 19 1_555 -0.330 -3.742 -0.130 -1.401 7.296 93.696 3 A_DG15:DG19_A A 15 ? A 19 ? 6 3 1 A DG 7 1_555 A DG 18 1_555 -0.060 -3.586 0.397 4.514 -8.140 101.683 4 A_DG7:DG18_A A 7 ? A 18 ? 6 3 1 A DG 3 1_555 A DG 16 1_555 0.521 3.958 -0.030 -9.924 10.210 -87.026 5 A_DG3:DG16_A A 3 ? A 16 ? 6 3 # 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 DT 11 1_555 A DT 13 1_555 A DG 20 1_555 A DG 14 1_555 -0.503 3.848 -3.439 -6.802 31.547 92.083 3.079 0.445 -2.321 21.404 4.615 96.360 1 AA_DT11DG20:DG14DT13_AA A 11 ? A 13 ? A 20 ? A 14 ? 1 A DG 20 1_555 A DG 14 1_555 A DG 15 1_555 A DG 19 1_555 -0.660 -4.228 -1.043 96.744 -150.195 157.870 -2.173 0.292 -0.410 -75.108 -48.379 179.742 2 AA_DG20DG15:DG19DG14_AA A 20 ? A 14 ? A 15 ? A 19 ? 1 A DG 15 1_555 A DG 19 1_555 A DG 7 1_555 A DG 18 1_555 -2.904 -0.718 1.342 -16.732 173.506 -66.690 -0.297 -1.516 1.102 -88.027 -8.489 -175.248 3 AA_DG15DG7:DG18DG19_AA A 15 ? A 19 ? A 7 ? A 18 ? 1 A DG 7 1_555 A DG 18 1_555 A DG 3 1_555 A DG 16 1_555 -2.280 -2.994 0.098 12.756 -2.502 178.627 -1.497 1.140 0.095 -1.251 -6.379 178.635 4 AA_DG7DG3:DG16DG18_AA A 7 ? A 18 ? A 3 ? A 16 ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model VNMRS _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 5J05 _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_