data_1Q2T # _entry.id 1Q2T # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1Q2T pdb_00001q2t 10.2210/pdb1q2t/pdb RCSB RCSB019844 ? ? WWPDB D_1000019844 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1RME _pdbx_database_related.details 'i-motif tetramer of 5mCCTCC' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Q2T _pdbx_database_status.recvd_initial_deposition_date 2003-07-26 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _audit_author.name 'Leroy, J.-L.' _audit_author.pdbx_ordinal 1 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'T.T pair intercalation and duplex inter-conversion within i-motif tetramers' J.Mol.Biol. 333 125 139 2003 JMOBAK UK 0022-2836 0070 ? 14516748 '10.1016/S0022-2836(03)00945-8' 1 'Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.' J.Mol.Biol. 261 399 414 1996 JMOBAK UK 0022-2836 0070 ? ? 10.1006/jmbi.1996.0472 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Leroy, J.-L.' 1 ? 1 'Nonin, S.' 2 ? 1 'Leroy, J.-L.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3'" _entity.formula_weight 1943.384 _entity.pdbx_number_of_molecules 4 _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 yes _entity_poly.pdbx_seq_one_letter_code '(MCY)(DC)(DT)(DC)(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can CCTCTCC _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 MCY n 1 2 DC n 1 3 DT n 1 4 DC n 1 5 DT n 1 6 DC n 1 7 DC n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 1Q2T _struct_ref.pdbx_db_accession 1Q2T _struct_ref.entity_id 1 _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 1Q2T A 1 ? 7 ? 1Q2T 1 ? 7 ? 1 7 2 1 1Q2T B 1 ? 7 ? 1Q2T 1 ? 7 ? 1 7 3 1 1Q2T C 1 ? 7 ? 1Q2T 1 ? 7 ? 1 7 4 1 1Q2T D 1 ? 7 ? 1Q2T 1 ? 7 ? 1 7 # 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 MCY 'DNA linking' n "5-METHYL-2'-DEOXYCYTIDINE" ? 'C10 H15 N3 O4' 241.244 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 '2D TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 273 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 4.4 _pdbx_nmr_exptl_sample_conditions.ionic_strength 'No added counter-ions' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '10mM DNA strand' _pdbx_nmr_sample_details.solvent_system 'H2O 90%, D2O 10%' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1Q2T _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ;the structure is based on a total of 172 restraints. 30 base-pairing restraints from hydrogen bonds, 78 NOE-distance restraints and 36 repulsive restraints reflecting the absence of NOE ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1Q2T _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _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 ? # 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 'structure solution' Brunger 1 X-PLOR 3.851 refinement Brunger 2 # _exptl.entry_id 1Q2T _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1Q2T _struct.title 'Solution structure of d(5mCCTCTCC)4' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Q2T _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA solution structure; i-motif; protonated cytidine; hemiprotonated base-pairs, DNA' # 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_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A MCY 1 "O3'" ? ? ? 1_555 A DC 2 P ? ? A MCY 1 A DC 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale both ? B MCY 1 "O3'" ? ? ? 1_555 B DC 2 P ? ? B MCY 1 B DC 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale3 covale both ? C MCY 1 "O3'" ? ? ? 1_555 C DC 2 P ? ? C MCY 1 C DC 2 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale4 covale both ? D MCY 1 "O3'" ? ? ? 1_555 D DC 2 P ? ? D MCY 1 D DC 2 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A MCY 1 N3 ? ? ? 1_555 C MCY 1 N4 ? ? A MCY 1 C MCY 1 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog2 hydrog ? ? A MCY 1 N4 ? ? ? 1_555 C MCY 1 N3 ? ? A MCY 1 C MCY 1 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N3 ? ? ? 1_555 C DC 2 N4 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog4 hydrog ? ? A DC 2 N4 ? ? ? 1_555 C DC 2 N3 ? ? A DC 2 C DC 2 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog5 hydrog ? ? A DT 3 N3 ? ? ? 1_555 C DT 3 O4 ? ? A DT 3 C DT 3 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog6 hydrog ? ? A DT 3 O4 ? ? ? 1_555 C DT 3 N3 ? ? A DT 3 C DT 3 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog7 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DC 4 N4 ? ? A DC 4 B DC 4 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog8 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DC 4 N3 ? ? A DC 4 B DC 4 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 C DC 4 N4 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 C DC 4 N3 ? ? A DC 4 C DC 4 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 C DT 5 O4 ? ? A DT 5 C DT 5 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 C DT 5 N3 ? ? A DT 5 C DT 5 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog13 hydrog ? ? A DC 6 N4 ? ? ? 1_555 C DC 6 O2 ? ? A DC 6 C DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog14 hydrog ? ? A DC 6 O2 ? ? ? 1_555 C DC 6 N4 ? ? A DC 6 C DC 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog15 hydrog ? ? A DC 7 N4 ? ? ? 1_555 C DC 7 O2 ? ? A DC 7 C DC 7 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog16 hydrog ? ? A DC 7 O2 ? ? ? 1_555 C DC 7 N4 ? ? A DC 7 C DC 7 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? B MCY 1 N3 ? ? ? 1_555 D MCY 1 N4 ? ? B MCY 1 D MCY 1 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog18 hydrog ? ? B MCY 1 N4 ? ? ? 1_555 D MCY 1 N3 ? ? B MCY 1 D MCY 1 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog19 hydrog ? ? B DC 2 N3 ? ? ? 1_555 D DC 2 N4 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog20 hydrog ? ? B DC 2 N4 ? ? ? 1_555 D DC 2 N3 ? ? B DC 2 D DC 2 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog21 hydrog ? ? B DT 3 O2 ? ? ? 1_555 B DC 4 N4 ? ? B DT 3 B DC 4 1_555 ? ? ? ? ? ? 'DT-DC MISPAIR' ? ? ? hydrog22 hydrog ? ? B DC 4 N3 ? ? ? 1_555 D DC 4 N4 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog23 hydrog ? ? B DC 4 N4 ? ? ? 1_555 D DC 4 N3 ? ? B DC 4 D DC 4 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog24 hydrog ? ? B DC 6 N3 ? ? ? 1_555 D DC 6 N4 ? ? B DC 6 D DC 6 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog25 hydrog ? ? B DC 6 N4 ? ? ? 1_555 D DC 6 N3 ? ? B DC 6 D DC 6 1_555 ? ? ? ? ? ? TYPE_14_PAIR ? ? ? hydrog26 hydrog ? ? B DC 7 N4 ? ? ? 1_555 D DC 7 O2 ? ? B DC 7 D DC 7 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog27 hydrog ? ? B DC 7 O2 ? ? ? 1_555 D DC 7 N4 ? ? B DC 7 D DC 7 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog28 hydrog ? ? C DC 4 N3 ? ? ? 1_555 D DC 4 N4 ? ? C DC 4 D DC 4 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 1Q2T _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MCY 1 1 1 MCY MCY A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DC 7 7 7 DC C A . n B 1 1 MCY 1 1 1 MCY MCY B . n B 1 2 DC 2 2 2 DC C B . n B 1 3 DT 3 3 3 DT T B . n B 1 4 DC 4 4 4 DC C B . n B 1 5 DT 5 5 5 DT T B . n B 1 6 DC 6 6 6 DC C B . n B 1 7 DC 7 7 7 DC C B . n C 1 1 MCY 1 1 1 MCY MCY C . n C 1 2 DC 2 2 2 DC C C . n C 1 3 DT 3 3 3 DT T C . n C 1 4 DC 4 4 4 DC C C . n C 1 5 DT 5 5 5 DT T C . n C 1 6 DC 6 6 6 DC C C . n C 1 7 DC 7 7 7 DC C C . n D 1 1 MCY 1 1 1 MCY MCY D . n D 1 2 DC 2 2 2 DC C D . n D 1 3 DT 3 3 3 DT T D . n D 1 4 DC 4 4 4 DC C D . n D 1 5 DT 5 5 5 DT T D . n D 1 6 DC 6 6 6 DC C D . n D 1 7 DC 7 7 7 DC C D . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MCY 1 A MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 2 B MCY 1 B MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 3 C MCY 1 C MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" 4 D MCY 1 D MCY 1 ? DC "5-METHYL-2'-DEOXYCYTIDINE" # _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 # 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 2003-09-23 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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' # 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 # 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' # 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 DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 110.67 108.30 2.37 0.30 N 2 1 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.22 119.90 3.32 0.50 N 3 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.94 108.30 2.64 0.30 N 4 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 110.33 108.30 2.03 0.30 N 5 1 C2 A DC 4 ? ? N3 A DC 4 ? ? C4 A DC 4 ? ? 123.44 119.90 3.54 0.50 N 6 1 N1 A DC 4 ? ? C2 A DC 4 ? ? O2 A DC 4 ? ? 122.91 118.90 4.01 0.60 N 7 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 110.25 108.30 1.95 0.30 N 8 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 110.79 108.30 2.49 0.30 N 9 1 C2 A DC 6 ? ? N3 A DC 6 ? ? C4 A DC 6 ? ? 123.13 119.90 3.23 0.50 N 10 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 111.38 108.30 3.08 0.30 N 11 1 C2 A DC 7 ? ? N3 A DC 7 ? ? C4 A DC 7 ? ? 123.14 119.90 3.24 0.50 N 12 1 "O4'" B DC 2 ? ? "C1'" B DC 2 ? ? N1 B DC 2 ? ? 110.54 108.30 2.24 0.30 N 13 1 C2 B DC 2 ? ? N3 B DC 2 ? ? C4 B DC 2 ? ? 123.22 119.90 3.32 0.50 N 14 1 N1 B DC 2 ? ? C2 B DC 2 ? ? O2 B DC 2 ? ? 122.83 118.90 3.93 0.60 N 15 1 "O4'" B DT 3 ? ? "C1'" B DT 3 ? ? N1 B DT 3 ? ? 110.79 108.30 2.49 0.30 N 16 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 110.62 108.30 2.32 0.30 N 17 1 N1 B DC 4 ? ? C2 B DC 4 ? ? O2 B DC 4 ? ? 122.67 118.90 3.77 0.60 N 18 1 "O4'" B DT 5 ? ? "C1'" B DT 5 ? ? N1 B DT 5 ? ? 111.08 108.30 2.78 0.30 N 19 1 "O4'" B DC 6 ? ? "C1'" B DC 6 ? ? N1 B DC 6 ? ? 110.99 108.30 2.69 0.30 N 20 1 C2 B DC 6 ? ? N3 B DC 6 ? ? C4 B DC 6 ? ? 123.03 119.90 3.13 0.50 N 21 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.93 108.30 2.63 0.30 N 22 1 C2 B DC 7 ? ? N3 B DC 7 ? ? C4 B DC 7 ? ? 123.05 119.90 3.15 0.50 N 23 1 "O4'" C DC 2 ? ? "C1'" C DC 2 ? ? N1 C DC 2 ? ? 110.72 108.30 2.42 0.30 N 24 1 "O4'" C DT 3 ? ? "C1'" C DT 3 ? ? N1 C DT 3 ? ? 110.98 108.30 2.68 0.30 N 25 1 "O4'" C DC 4 ? ? "C1'" C DC 4 ? ? N1 C DC 4 ? ? 110.31 108.30 2.01 0.30 N 26 1 "O4'" C DT 5 ? ? "C1'" C DT 5 ? ? N1 C DT 5 ? ? 110.30 108.30 2.00 0.30 N 27 1 "O4'" C DC 6 ? ? "C1'" C DC 6 ? ? N1 C DC 6 ? ? 110.80 108.30 2.50 0.30 N 28 1 "O4'" C DC 7 ? ? "C1'" C DC 7 ? ? N1 C DC 7 ? ? 111.24 108.30 2.94 0.30 N 29 1 "O4'" D DC 2 ? ? "C1'" D DC 2 ? ? N1 D DC 2 ? ? 110.43 108.30 2.13 0.30 N 30 1 "O4'" D DT 3 ? ? "C1'" D DT 3 ? ? N1 D DT 3 ? ? 110.65 108.30 2.35 0.30 N 31 1 "O4'" D DC 4 ? ? "C1'" D DC 4 ? ? N1 D DC 4 ? ? 110.36 108.30 2.06 0.30 N 32 1 "O4'" D DT 5 ? ? "C1'" D DT 5 ? ? N1 D DT 5 ? ? 110.88 108.30 2.58 0.30 N 33 1 "O4'" D DC 6 ? ? "C1'" D DC 6 ? ? N1 D DC 6 ? ? 111.64 108.30 3.34 0.30 N 34 1 "O4'" D DC 7 ? ? "C1'" D DC 7 ? ? N1 D DC 7 ? ? 110.98 108.30 2.68 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DC B 2 ? ? 0.071 'SIDE CHAIN' 2 1 DC D 2 ? ? 0.063 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1Q2T 'quadruple helix' 1Q2T 'parallel strands' 1Q2T '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 DC 7 1_555 C DC 7 1_555 -2.145 -1.916 0.079 24.851 20.932 -179.060 1 A_DC7:DC7_C A 7 ? C 7 ? 15 2 1 D MCY 1 1_555 B MCY 1 1_555 -2.031 -0.024 -0.006 -15.554 -26.415 -179.765 2 D_MCY1:MCY1_B D 1 ? B 1 ? 14 2 1 A DC 6 1_555 C DC 6 1_555 -2.190 -2.024 -0.083 2.295 -19.457 -179.846 3 A_DC6:DC6_C A 6 ? C 6 ? 15 2 1 D DC 2 1_555 B DC 2 1_555 -2.129 -0.217 -0.073 14.049 -4.505 -179.762 4 D_DC2:DC2_B D 2 ? B 2 ? 14 2 1 A DT 5 1_555 C DT 5 1_555 1.456 -0.499 -0.119 16.974 23.090 179.884 5 A_DT5:DT5_C A 5 ? C 5 ? 12 2 1 C DC 4 1_555 A DC 4 1_555 2.237 0.001 0.381 26.737 5.745 176.334 6 C_DC4:DC4_A C 4 ? A 4 ? 14 2 1 B DC 4 1_555 D DC 4 1_555 1.896 0.334 -0.101 -9.356 35.472 178.912 7 B_DC4:DC4_D B 4 ? D 4 ? 14 2 1 C DT 3 1_555 A DT 3 1_555 -1.309 0.366 -0.201 -4.202 -16.685 -178.309 8 C_DT3:DT3_A C 3 ? A 3 ? 12 2 1 A DC 2 1_555 C DC 2 1_555 2.015 0.432 0.094 20.912 10.916 179.000 9 A_DC2:DC2_C A 2 ? C 2 ? 14 2 1 D DC 6 1_555 B DC 6 1_555 1.748 0.889 -0.141 -28.293 -40.250 178.564 10 D_DC6:DC6_B D 6 ? B 6 ? 14 2 1 A MCY 1 1_555 C MCY 1 1_555 2.095 0.062 -0.108 -3.851 1.224 179.626 11 A_MCY1:MCY1_C A 1 ? C 1 ? 14 2 1 D DC 7 1_555 B DC 7 1_555 -1.919 -1.628 -0.007 8.272 22.326 -179.912 12 D_DC7:DC7_B D 7 ? B 7 ? 15 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 DC 7 1_555 C DC 7 1_555 D MCY 1 1_555 B MCY 1 1_555 1.815 -2.039 -0.060 132.601 119.870 63.339 -0.999 -0.930 -0.049 60.134 -66.521 178.937 1 AD_DC7MCY1:MCY1DC7_BC A 7 ? C 7 ? D 1 ? B 1 ? 1 D MCY 1 1_555 B MCY 1 1_555 A DC 6 1_555 C DC 6 1_555 -3.132 3.180 -0.001 128.235 125.439 -115.383 -1.591 -1.565 0.008 -62.753 64.152 -179.672 2 DA_MCY1DC6:DC6MCY1_CB D 1 ? B 1 ? A 6 ? C 6 ? 1 A DC 6 1_555 C DC 6 1_555 D DC 2 1_555 B DC 2 1_555 -1.312 2.145 -0.115 -153.820 -90.531 35.875 1.052 0.690 0.005 -45.532 77.362 178.558 3 AD_DC6DC2:DC2DC6_BC A 6 ? C 6 ? D 2 ? B 2 ? 1 D DC 2 1_555 B DC 2 1_555 A DT 5 1_555 C DT 5 1_555 2.326 2.705 -0.043 136.173 -115.595 60.481 1.344 -1.173 -0.002 -58.019 -68.347 178.808 4 DA_DC2DT5:DT5DC2_CB D 2 ? B 2 ? A 5 ? C 5 ? 1 A DT 5 1_555 C DT 5 1_555 C DC 4 1_555 A DC 4 1_555 0.084 -0.077 -2.710 2.195 -1.926 149.275 -0.046 -0.051 -2.709 -0.999 -1.138 149.285 5 AC_DT5DC4:DC4DT5_AC A 5 ? C 5 ? C 4 ? A 4 ? 1 C DC 4 1_555 A DC 4 1_555 B DC 4 1_555 D DC 4 1_555 -1.022 1.620 0.035 -141.397 -103.535 93.530 0.807 0.516 -0.065 -52.148 71.218 176.747 6 CB_DC4DC4:DC4DC4_DA C 4 ? A 4 ? B 4 ? D 4 ? 1 B DC 4 1_555 D DC 4 1_555 C DT 3 1_555 A DT 3 1_555 2.822 3.714 -0.028 140.129 -111.520 -169.640 -1.858 1.410 -0.018 55.761 70.066 -179.918 7 BC_DC4DT3:DT3DC4_AD B 4 ? D 4 ? C 3 ? A 3 ? 1 C DT 3 1_555 A DT 3 1_555 A DC 2 1_555 C DC 2 1_555 0.031 0.030 -2.865 1.635 0.825 -23.598 0.168 -0.401 -2.860 -2.013 3.990 -23.668 8 CA_DT3DC2:DC2DT3_CA C 3 ? A 3 ? A 2 ? C 2 ? 1 A DC 2 1_555 C DC 2 1_555 D DC 6 1_555 B DC 6 1_555 -2.680 3.707 0.622 -131.352 -121.322 -29.254 -1.511 -1.711 0.686 60.963 -66.003 -178.847 9 AD_DC2DC6:DC6DC2_BC A 2 ? C 2 ? D 6 ? B 6 ? 1 D DC 6 1_555 B DC 6 1_555 A MCY 1 1_555 C MCY 1 1_555 -2.300 1.943 -0.148 121.598 127.281 -66.112 -0.957 -1.164 0.074 -64.293 61.422 -176.673 10 DA_DC6MCY1:MCY1DC6_CB D 6 ? B 6 ? A 1 ? C 1 ? 1 A MCY 1 1_555 C MCY 1 1_555 D DC 7 1_555 B DC 7 1_555 -2.589 -2.426 0.256 116.721 -135.291 136.071 -1.173 1.330 0.292 -67.682 -58.392 179.507 11 AD_MCY1DC7:DC7MCY1_BC A 1 ? C 1 ? D 7 ? B 7 ? #