data_225D # _entry.id 225D # _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 225D pdb_0000225d 10.2210/pdb225d/pdb WWPDB D_1000177600 ? ? # 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 1995-10-15 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 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 4 'Structure model' Other 6 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_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 5 'Structure model' chem_comp_atom 6 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 225D _pdbx_database_status.recvd_initial_deposition_date 1995-07-12 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gehring, K.' 1 'Leroy, J.L.' 2 'Gueron, M.' 3 # _citation.id primary _citation.title 'A tetrameric DNA structure with protonated cytosine.cytosine base pairs.' _citation.journal_abbrev Nature _citation.journal_volume 363 _citation.page_first 561 _citation.page_last 565 _citation.year 1993 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 8389423 _citation.pdbx_database_id_DOI 10.1038/363561a0 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gehring, K.' 1 ? primary 'Leroy, J.L.' 2 ? primary 'Gueron, M.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*TP*CP*CP*CP*CP*C)-3') ; _entity.formula_weight 1705.145 _entity.pdbx_number_of_molecules 4 _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 '(DT)(DC)(DC)(DC)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can TCCCCC _entity_poly.pdbx_strand_id A,B,C,D _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 DT n 1 2 DC n 1 3 DC n 1 4 DC n 1 5 DC n 1 6 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 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 DT 1 1 1 DT T A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DC 6 6 6 DC C A . n B 1 1 DT 1 1 1 DT T B . n B 1 2 DC 2 2 2 DC C B . n B 1 3 DC 3 3 3 DC C B . n B 1 4 DC 4 4 4 DC C B . n B 1 5 DC 5 5 5 DC C B . n B 1 6 DC 6 6 6 DC C B . n C 1 1 DT 1 1 1 DT T C . n C 1 2 DC 2 2 2 DC C C . n C 1 3 DC 3 3 3 DC C C . n C 1 4 DC 4 4 4 DC C C . n C 1 5 DC 5 5 5 DC C C . n C 1 6 DC 6 6 6 DC C C . n D 1 1 DT 1 1 1 DT T D . n D 1 2 DC 2 2 2 DC C D . n D 1 3 DC 3 3 3 DC C D . n D 1 4 DC 4 4 4 DC C D . n D 1 5 DC 5 5 5 DC C D . n D 1 6 DC 6 6 6 DC C D . n # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement . ? 2 X-PLOR phasing . ? 3 # _cell.entry_id 225D _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 225D _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 225D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _database_PDB_matrix.entry_id 225D _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 225D _struct.title 'A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 225D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, INTERCALATED CYTOSINE TETRAD' # 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 ? C N N 1 ? D N N 1 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 225D _struct_ref.pdbx_db_accession 225D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 225D A 1 ? 6 ? 225D 1 ? 6 ? 1 6 2 1 225D B 1 ? 6 ? 225D 1 ? 6 ? 1 6 3 1 225D C 1 ? 6 ? 225D 1 ? 6 ? 1 6 4 1 225D D 1 ? 6 ? 225D 1 ? 6 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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 hydrog1 hydrog ? ? A DT 1 N3 ? ? ? 1_555 C DT 1 O2 ? ? A DT 1 C DT 1 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog2 hydrog ? ? A DT 1 O2 ? ? ? 1_555 C DT 1 N3 ? ? A DT 1 C DT 1 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DC 2 O2 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 C DC 2 N4 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 C DC 3 O2 ? ? A DC 3 C DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 C DC 3 N4 ? ? A DC 3 C DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DC 4 O2 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? A DC 4 O2 ? ? ? 1_555 C DC 4 N4 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? A DC 5 N4 ? ? ? 1_555 C DC 5 O2 ? ? A DC 5 C DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog10 hydrog ? ? A DC 5 O2 ? ? ? 1_555 C DC 5 N4 ? ? A DC 5 C DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog11 hydrog ? ? A DC 6 N4 ? ? ? 1_555 C DC 6 O2 ? ? A DC 6 C DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog12 hydrog ? ? A DC 6 O2 ? ? ? 1_555 C DC 6 N4 ? ? A DC 6 C DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog13 hydrog ? ? B DT 1 N3 ? ? ? 1_555 D DT 1 O2 ? ? B DT 1 D DT 1 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog14 hydrog ? ? B DT 1 O2 ? ? ? 1_555 D DT 1 N3 ? ? B DT 1 D DT 1 1_555 ? ? ? ? ? ? TYPE_13_PAIR ? ? ? hydrog15 hydrog ? ? B DC 2 N4 ? ? ? 1_555 D DC 2 O2 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog16 hydrog ? ? B DC 2 O2 ? ? ? 1_555 D DC 2 N4 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? B DC 3 N4 ? ? ? 1_555 D DC 3 O2 ? ? B DC 3 D DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? B DC 3 O2 ? ? ? 1_555 D DC 3 N4 ? ? B DC 3 D DC 3 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog19 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DC 4 O2 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog20 hydrog ? ? B DC 4 O2 ? ? ? 1_555 D DC 4 N4 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog21 hydrog ? ? B DC 5 N4 ? ? ? 1_555 D DC 5 O2 ? ? B DC 5 D DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog22 hydrog ? ? B DC 5 O2 ? ? ? 1_555 D DC 5 N4 ? ? B DC 5 D DC 5 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog23 hydrog ? ? B DC 6 N4 ? ? ? 1_555 D DC 6 O2 ? ? B DC 6 D DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog24 hydrog ? ? B DC 6 O2 ? ? ? 1_555 D DC 6 N4 ? ? B DC 6 D DC 6 1_555 ? ? ? ? ? ? TYPE_15_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 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 112.12 108.30 3.82 0.30 N 2 1 C6 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 119.12 122.90 -3.78 0.60 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 112.67 108.30 4.37 0.30 N 4 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 112.97 108.30 4.67 0.30 N 5 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 112.03 108.30 3.73 0.30 N 6 1 "O4'" B DT 1 ? ? "C1'" B DT 1 ? ? N1 B DT 1 ? ? 112.06 108.30 3.76 0.30 N 7 1 C6 B DT 1 ? ? C5 B DT 1 ? ? C7 B DT 1 ? ? 119.08 122.90 -3.82 0.60 N 8 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 112.68 108.30 4.38 0.30 N 9 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 112.98 108.30 4.68 0.30 N 10 1 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 112.02 108.30 3.72 0.30 N 11 1 "O4'" C DT 1 ? ? "C1'" C DT 1 ? ? N1 C DT 1 ? ? 112.10 108.30 3.80 0.30 N 12 1 C6 C DT 1 ? ? C5 C DT 1 ? ? C7 C DT 1 ? ? 119.09 122.90 -3.81 0.60 N 13 1 "O4'" C DC 2 ? ? "C1'" C DC 2 ? ? N1 C DC 2 ? ? 112.61 108.30 4.31 0.30 N 14 1 "O4'" C DC 3 ? ? "C1'" C DC 3 ? ? N1 C DC 3 ? ? 112.95 108.30 4.65 0.30 N 15 1 "O4'" C DC 6 ? ? "C1'" C DC 6 ? ? N1 C DC 6 ? ? 112.05 108.30 3.75 0.30 N 16 1 "O4'" D DT 1 ? ? "C1'" D DT 1 ? ? N1 D DT 1 ? ? 112.07 108.30 3.77 0.30 N 17 1 C6 D DT 1 ? ? C5 D DT 1 ? ? C7 D DT 1 ? ? 119.07 122.90 -3.83 0.60 N 18 1 "O4'" D DC 2 ? ? "C1'" D DC 2 ? ? N1 D DC 2 ? ? 112.67 108.30 4.37 0.30 N 19 1 "O4'" D DC 3 ? ? "C1'" D DC 3 ? ? N1 D DC 3 ? ? 112.96 108.30 4.66 0.30 N 20 1 "O4'" D DC 6 ? ? "C1'" D DC 6 ? ? N1 D DC 6 ? ? 112.07 108.30 3.77 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 1 ? ? 0.075 'SIDE CHAIN' 2 1 DT B 1 ? ? 0.075 'SIDE CHAIN' 3 1 DT C 1 ? ? 0.074 'SIDE CHAIN' 4 1 DT D 1 ? ? 0.075 'SIDE CHAIN' # _pdbx_nmr_ensemble.entry_id 225D _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_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 4.3 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_details.entry_id 225D _pdbx_nmr_details.text ;DATA COLLECTION PARAMETERS: FREQUENCY: 600 MHZ FOR 1H, 242 MHZ FOR 31P SAMPLE TUBE: 5 MM, 7.5 MILLIMOLAR STRAND, PH 4.3, 25 C SPECTRA FOR ASSIGNMENTS: HOMONUCLEAR PROTON 2D, 1H-31P TOCSY; SPECTRA FOR CONSTRAINTS: NOESY, DQF-COSY, 1H-31P COSY ; # _pdbx_nmr_constraints.entry_id 225D _pdbx_nmr_constraints.NOE_constraints_total 70 _pdbx_nmr_constraints.NOE_intraresidue_total_count 43 _pdbx_nmr_constraints.NOE_sequential_total_count 6 _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count 15 _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? # _pdbx_nmr_refine.entry_id 225D _pdbx_nmr_refine.method 'MOLECULAR DYNAMICS, ENERGY MINIMIZATION' _pdbx_nmr_refine.details ;STRUCTURE CALCULATION: MOLECULAR DYNAMICS AND ENERGY MINIMIZATION USING X-PLOR CONSTRAINTS (PER STRAND): TOTAL 70 DISTANCE CONSTRAINTS (ABOUT 12/NUCLEOTIDE) 43 FROM INTRANUCLEOTIDE NOES 6 FROM SEQUENTIAL INTERNUCLEOTIDE NOES 21 FROM NON-SEQUENTIAL INTERNUCLEOTIDE NOES 15 FROM HYDROGEN BONDS DIHEDRAL ANGLE CONSTRAINTS 10 BACKBONE AND SUGAR RING TORSION ANGLES CONSTRAINTS TO MAKE CYTOSINE BASE PAIRS PLANAR 4-FOLD SYMMETRY CONSTRAINTS (AS 3 SETS OF PAIRWISE NON-CRYSTALLOGRAPHIC SYMMETRY CONSTRAINTS) ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors BRUNGER _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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DT OP3 O N N 35 DT P P N N 36 DT OP1 O N N 37 DT OP2 O N N 38 DT "O5'" O N N 39 DT "C5'" C N N 40 DT "C4'" C N R 41 DT "O4'" O N N 42 DT "C3'" C N S 43 DT "O3'" O N N 44 DT "C2'" C N N 45 DT "C1'" C N R 46 DT N1 N N N 47 DT C2 C N N 48 DT O2 O N N 49 DT N3 N N N 50 DT C4 C N N 51 DT O4 O N N 52 DT C5 C N N 53 DT C7 C N N 54 DT C6 C N N 55 DT HOP3 H N N 56 DT HOP2 H N N 57 DT "H5'" H N N 58 DT "H5''" H N N 59 DT "H4'" H N N 60 DT "H3'" H N N 61 DT "HO3'" H N N 62 DT "H2'" H N N 63 DT "H2''" H N N 64 DT "H1'" H N N 65 DT H3 H N N 66 DT H71 H N N 67 DT H72 H N N 68 DT H73 H N N 69 DT H6 H N N 70 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DT OP3 P sing N N 36 DT OP3 HOP3 sing N N 37 DT P OP1 doub N N 38 DT P OP2 sing N N 39 DT P "O5'" sing N N 40 DT OP2 HOP2 sing N N 41 DT "O5'" "C5'" sing N N 42 DT "C5'" "C4'" sing N N 43 DT "C5'" "H5'" sing N N 44 DT "C5'" "H5''" sing N N 45 DT "C4'" "O4'" sing N N 46 DT "C4'" "C3'" sing N N 47 DT "C4'" "H4'" sing N N 48 DT "O4'" "C1'" sing N N 49 DT "C3'" "O3'" sing N N 50 DT "C3'" "C2'" sing N N 51 DT "C3'" "H3'" sing N N 52 DT "O3'" "HO3'" sing N N 53 DT "C2'" "C1'" sing N N 54 DT "C2'" "H2'" sing N N 55 DT "C2'" "H2''" sing N N 56 DT "C1'" N1 sing N N 57 DT "C1'" "H1'" sing N N 58 DT N1 C2 sing N N 59 DT N1 C6 sing N N 60 DT C2 O2 doub N N 61 DT C2 N3 sing N N 62 DT N3 C4 sing N N 63 DT N3 H3 sing N N 64 DT C4 O4 doub N N 65 DT C4 C5 sing N N 66 DT C5 C7 sing N N 67 DT C5 C6 doub N N 68 DT C7 H71 sing N N 69 DT C7 H72 sing N N 70 DT C7 H73 sing N N 71 DT C6 H6 sing N N 72 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 225D 'double helix' 225D 'parallel strands' 225D 'mismatched base pair' # 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 1 1_555 C DT 1 1_555 1.971 2.689 0.000 -7.686 10.837 179.998 1 A_DT1:DT1_C A 1 ? C 1 ? 13 2 1 D DC 6 1_555 B DC 6 1_555 -2.051 -1.333 0.000 -0.918 1.045 -179.981 2 D_DC6:DC6_B D 6 ? B 6 ? 15 2 1 A DC 2 1_555 C DC 2 1_555 1.976 1.217 0.000 -5.235 0.997 179.980 3 A_DC2:DC2_C A 2 ? C 2 ? 15 2 1 D DC 5 1_555 B DC 5 1_555 1.923 1.075 0.000 -4.031 0.730 179.997 4 D_DC5:DC5_B D 5 ? B 5 ? 15 2 1 A DC 3 1_555 C DC 3 1_555 -1.800 -1.070 0.000 -0.850 1.851 -179.977 5 A_DC3:DC3_C A 3 ? C 3 ? 15 2 1 D DC 4 1_555 B DC 4 1_555 2.000 1.197 0.000 0.214 1.154 179.996 6 D_DC4:DC4_B D 4 ? B 4 ? 15 2 1 A DC 4 1_555 C DC 4 1_555 -2.000 -1.197 -0.001 -0.213 -1.051 -179.991 7 A_DC4:DC4_C A 4 ? C 4 ? 15 2 1 D DC 3 1_555 B DC 3 1_555 1.800 1.067 0.000 0.846 -1.891 179.982 8 D_DC3:DC3_B D 3 ? B 3 ? 15 2 1 A DC 5 1_555 C DC 5 1_555 -1.923 -1.076 0.000 3.983 -0.722 -179.980 9 A_DC5:DC5_C A 5 ? C 5 ? 15 2 1 D DC 2 1_555 B DC 2 1_555 -1.976 -1.219 0.000 5.309 -0.889 -179.998 10 D_DC2:DC2_B D 2 ? B 2 ? 15 2 1 A DC 6 1_555 C DC 6 1_555 2.050 1.324 -0.001 0.885 -1.015 179.913 11 A_DC6:DC6_C A 6 ? C 6 ? 15 2 1 D DT 1 1_555 B DT 1 1_555 -1.970 -2.688 0.000 7.689 -10.822 -179.993 12 D_DT1:DT1_B D 1 ? B 1 ? 13 2 # 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 1 1_555 C DT 1 1_555 D DC 6 1_555 B DC 6 1_555 2.532 2.017 -0.001 112.151 -140.777 57.245 1.008 -1.266 0.000 -70.391 -56.077 179.990 1 AD_DT1DC6:DC6DT1_BC A 1 ? C 1 ? D 6 ? B 6 ? 1 D DC 6 1_555 B DC 6 1_555 A DC 2 1_555 C DC 2 1_555 -2.529 -1.640 -0.001 97.919 -151.031 51.125 -0.820 1.265 0.000 -75.517 -48.960 179.996 2 DA_DC6DC2:DC2DC6_CB D 6 ? B 6 ? A 2 ? C 2 ? 1 A DC 2 1_555 C DC 2 1_555 D DC 5 1_555 B DC 5 1_555 -2.145 2.226 0.000 129.573 124.924 102.081 1.113 1.073 0.001 62.463 -64.788 179.992 3 AD_DC2DC5:DC5DC2_BC A 2 ? C 2 ? D 5 ? B 5 ? 1 D DC 5 1_555 B DC 5 1_555 A DC 3 1_555 C DC 3 1_555 2.578 1.739 0.000 -100.645 149.217 -15.745 -0.869 1.289 0.000 -74.613 -50.326 -179.987 4 DA_DC5DC3:DC3DC5_CB D 5 ? B 5 ? A 3 ? C 3 ? 1 A DC 3 1_555 C DC 3 1_555 D DC 4 1_555 B DC 4 1_555 2.353 1.974 -0.001 115.680 -137.886 118.719 0.987 -1.177 0.000 -68.944 -57.841 179.992 5 AD_DC3DC4:DC4DC3_BC A 3 ? C 3 ? D 4 ? B 4 ? 1 D DC 4 1_555 B DC 4 1_555 A DC 4 1_555 C DC 4 1_555 2.518 1.833 0.000 -105.956 145.505 -9.531 -0.917 1.259 0.000 -72.754 -52.979 -179.995 6 DA_DC4DC4:DC4DC4_CB D 4 ? B 4 ? A 4 ? C 4 ? 1 A DC 4 1_555 C DC 4 1_555 D DC 3 1_555 B DC 3 1_555 2.348 1.971 0.000 115.723 -137.864 -116.373 -0.986 1.174 0.000 68.932 57.862 -179.998 7 AD_DC4DC3:DC3DC4_BC A 4 ? C 4 ? D 3 ? B 3 ? 1 D DC 3 1_555 B DC 3 1_555 A DC 5 1_555 C DC 5 1_555 -2.579 -1.740 0.000 100.666 -149.207 76.740 -0.870 1.289 0.000 -74.605 -50.334 179.992 8 DA_DC3DC5:DC5DC3_CB D 3 ? B 3 ? A 5 ? C 5 ? 1 A DC 5 1_555 C DC 5 1_555 D DC 2 1_555 B DC 2 1_555 -2.142 2.224 -0.001 129.604 124.897 122.751 1.112 1.071 0.000 62.449 -64.802 179.995 9 AD_DC5DC2:DC2DC5_BC A 5 ? C 5 ? D 2 ? B 2 ? 1 D DC 2 1_555 B DC 2 1_555 A DC 6 1_555 C DC 6 1_555 2.530 1.644 0.002 -97.985 150.975 -172.572 -0.822 1.265 0.002 -75.488 -48.993 -179.999 10 DA_DC2DC6:DC6DC2_CB D 2 ? B 2 ? A 6 ? C 6 ? 1 A DC 6 1_555 C DC 6 1_555 D DT 1 1_555 B DT 1 1_555 2.532 2.018 -0.003 112.243 -140.701 155.740 1.009 -1.266 -0.003 -70.351 -56.122 179.997 11 AD_DC6DT1:DT1DC6_BC A 6 ? C 6 ? D 1 ? B 1 ? # _atom_sites.entry_id 225D _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_