data_7ZYX # _entry.id 7ZYX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.366 _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 7ZYX pdb_00007zyx 10.2210/pdb7zyx/pdb WWPDB D_1292123343 ? ? BMRB 34735 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details ;Dimeric i-motif from 2'Farabinocytidine-modified TC5 ; _pdbx_database_related.db_id 34735 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7ZYX _pdbx_database_status.recvd_initial_deposition_date 2022-05-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Garavis, M.' 1 0000-0003-1889-1713 'El Khoury, R.' 2 0000-0002-8068-4566 'Damha, M.J.' 3 0000-0002-4458-1623 'Gonzalez, C.' 4 0000-0001-8796-1282 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Commun Chem' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2399-3669 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 6 _citation.language ? _citation.page_first 31 _citation.page_last 31 _citation.title ;i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds. ; _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s42004-023-00831-7 _citation.pdbx_database_id_PubMed 36797370 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'El-Khoury, R.' 1 0000-0002-8068-4566 primary 'Macaluso, V.' 2 ? primary 'Hennecker, C.' 3 ? primary 'Mittermaier, A.K.' 4 ? primary 'Orozco, M.' 5 ? primary 'Gonzalez, C.' 6 0000-0001-8796-1282 primary 'Garavis, M.' 7 0000-0003-1889-1713 primary 'Damha, M.J.' 8 0000-0002-4458-1623 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*TP*(CFL)P*(CFL)P*(CFL)P*(CFL)P*(CFL))-3') ; _entity.formula_weight 1795.099 _entity.pdbx_number_of_molecules 2 _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 '(DT)(CFL)(CFL)(CFL)(CFL)(CFL)' _entity_poly.pdbx_seq_one_letter_code_can TCCCCC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 CFL n 1 3 CFL n 1 4 CFL n 1 5 CFL n 1 6 CFL 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 6 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7ZYX _struct_ref.pdbx_db_accession 7ZYX _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # 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 7ZYX A 1 ? 6 ? 7ZYX 1 ? 6 ? 1 6 2 1 7ZYX B 1 ? 6 ? 7ZYX 7 ? 12 ? 7 12 # 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 CFL 'DNA linking' n '4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one' "2'-FLUORO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" 'C9 H13 F N3 O7 P' 325.188 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # 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 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 2 isotropic 3 1 1 '2D DQF-COSY' 2 isotropic 4 1 1 '2D 1H-19F HOESY' 2 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 5.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 10 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label Conditions_1 _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '10 mM NaPi, 90% H2O/10% D2O' _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label TC5_sample _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 'AVANCE NEO' ? Bruker 600 ? 2 'AVANCE III HD' ? Bruker 600 ? # _pdbx_nmr_refine.entry_id 7ZYX _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 5 # _pdbx_nmr_ensemble.entry_id 7ZYX _pdbx_nmr_ensemble.conformers_calculated_total_number 45 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum' _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 7ZYX _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'chemical shift assignment' NMRFAM-SPARKY ? 'Lee W, Tonelli M, Markley JL.' 2 collection TopSpin ? 'Bruker Biospin' 3 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' 4 'peak picking' NMRFAM-SPARKY ? 'Lee W, Tonelli M, Markley JL.' 5 refinement Amber ? 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' # _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 7ZYX _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7ZYX _struct.title ;Dimeric i-motif from 2'Farabinocytidine-modified TC5 ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7ZYX _struct_keywords.text ;i-motif, FANA, 2'Farabinocytidine, DNA ; _struct_keywords.pdbx_keywords 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 ? # 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 DT 1 "O3'" ? ? ? 1_555 A CFL 2 P ? ? A DT 1 A CFL 2 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale2 covale one ? A CFL 2 "O3'" ? ? ? 1_555 A CFL 3 P ? ? A CFL 2 A CFL 3 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale one ? A CFL 3 "O3'" ? ? ? 1_555 A CFL 4 P ? ? A CFL 3 A CFL 4 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale4 covale one ? A CFL 4 "O3'" ? ? ? 1_555 A CFL 5 P ? ? A CFL 4 A CFL 5 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale5 covale one ? A CFL 5 "O3'" ? ? ? 1_555 A CFL 6 P ? ? A CFL 5 A CFL 6 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale6 covale both ? B DT 1 "O3'" ? ? ? 1_555 B CFL 2 P ? ? B DT 7 B CFL 8 1_555 ? ? ? ? ? ? ? 1.619 ? ? covale7 covale one ? B CFL 2 "O3'" ? ? ? 1_555 B CFL 3 P ? ? B CFL 8 B CFL 9 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale8 covale one ? B CFL 3 "O3'" ? ? ? 1_555 B CFL 4 P ? ? B CFL 9 B CFL 10 1_555 ? ? ? ? ? ? ? 1.621 ? ? covale9 covale one ? B CFL 4 "O3'" ? ? ? 1_555 B CFL 5 P ? ? B CFL 10 B CFL 11 1_555 ? ? ? ? ? ? ? 1.618 ? ? covale10 covale one ? B CFL 5 "O3'" ? ? ? 1_555 B CFL 6 P ? ? B CFL 11 B CFL 12 1_555 ? ? ? ? ? ? ? 1.619 ? ? hydrog1 hydrog ? ? A DT 1 N3 ? ? ? 1_555 B DT 1 O4 ? ? A DT 1 B DT 7 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 B DT 1 N3 ? ? A DT 1 B DT 7 1_555 ? ? ? ? ? ? TYPE_12_PAIR ? ? ? hydrog3 hydrog ? ? A CFL 2 N4 ? ? ? 1_555 B CFL 2 O2 ? ? A CFL 2 B CFL 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog4 hydrog ? ? A CFL 2 O2 ? ? ? 1_555 B CFL 2 N4 ? ? A CFL 2 B CFL 8 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog5 hydrog ? ? A CFL 3 N4 ? ? ? 1_555 B CFL 3 O2 ? ? A CFL 3 B CFL 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog6 hydrog ? ? A CFL 3 O2 ? ? ? 1_555 B CFL 3 N4 ? ? A CFL 3 B CFL 9 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog7 hydrog ? ? A CFL 4 N4 ? ? ? 1_555 B CFL 4 O2 ? ? A CFL 4 B CFL 10 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog8 hydrog ? ? A CFL 4 O2 ? ? ? 1_555 B CFL 4 N4 ? ? A CFL 4 B CFL 10 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog9 hydrog ? ? A CFL 5 N4 ? ? ? 1_555 B CFL 5 O2 ? ? A CFL 5 B CFL 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog10 hydrog ? ? A CFL 5 O2 ? ? ? 1_555 B CFL 5 N4 ? ? A CFL 5 B CFL 11 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog11 hydrog ? ? A CFL 6 N4 ? ? ? 1_555 B CFL 6 O2 ? ? A CFL 6 B CFL 12 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog12 hydrog ? ? A CFL 6 O2 ? ? ? 1_555 B CFL 6 N4 ? ? A CFL 6 B CFL 12 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 7ZYX _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C F 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 DT 1 1 1 DT DT A . n A 1 2 CFL 2 2 2 CFL CFL A . n A 1 3 CFL 3 3 3 CFL CFL A . n A 1 4 CFL 4 4 4 CFL CFL A . n A 1 5 CFL 5 5 5 CFL CFL A . n A 1 6 CFL 6 6 6 CFL CFL A . n B 1 1 DT 1 7 7 DT DT B . n B 1 2 CFL 2 8 8 CFL CFL B . n B 1 3 CFL 3 9 9 CFL CFL B . n B 1 4 CFL 4 10 10 CFL CFL B . n B 1 5 CFL 5 11 11 CFL CFL B . n B 1 6 CFL 6 12 12 CFL CFL B . n # loop_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 2 mgaravis@iqfr.csic.es Miguel Garavis ? 'principal investigator/group leader' 0000-0003-1889-1713 3 cgonzalez@iqfr.csic.es Carlos Gonzalez ? 'principal investigator/group leader' 0000-0001-8796-1282 4 masad.damha@mcgill.ca Masad Damha J 'principal investigator/group leader' 0000-0002-4458-1623 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # 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)' 4490 ? 1 MORE 38 ? 1 'SSA (A^2)' 780 ? # _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 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2023-03-01 # _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 ? # _pdbx_entry_details.entry_id 7ZYX _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component NaPi _pdbx_nmr_exptl_sample.concentration 10 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mM _pdbx_nmr_exptl_sample.isotopic_labeling 'natural abundance' # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 5 O1P B CFL 9 ? ? "HO3'" B CFL 12 ? ? 1.33 2 6 O1P B CFL 9 ? ? "HO3'" B CFL 12 ? ? 1.28 3 7 O1P B CFL 9 ? ? "HO3'" B CFL 12 ? ? 1.28 4 8 O1P B CFL 9 ? ? "HO3'" B CFL 12 ? ? 1.29 # 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 2 C6 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 118.83 122.90 -4.07 0.60 N 2 3 "O4'" A DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 110.43 108.30 2.13 0.30 N 3 4 C6 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 119.10 122.90 -3.80 0.60 N 4 4 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 119.26 122.90 -3.64 0.60 N 5 5 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 119.25 122.90 -3.65 0.60 N 6 7 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 110.61 108.30 2.31 0.30 N 7 8 C6 A DT 1 ? ? C5 A DT 1 ? ? C7 A DT 1 ? ? 119.29 122.90 -3.61 0.60 N 8 8 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 118.20 122.90 -4.70 0.60 N # _ndb_struct_conf_na.entry_id 7ZYX _ndb_struct_conf_na.feature 'double 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 1 1_555 B DT 1 1_555 -1.737 1.094 0.348 15.096 17.327 -177.958 1 A_DT1:DT7_B A 1 ? B 7 ? 12 2 1 A CFL 2 1_555 B CFL 2 1_555 2.060 1.656 0.174 -12.030 6.974 179.385 2 A_CFL2:CFL8_B A 2 ? B 8 ? 15 2 1 A CFL 6 1_555 B CFL 6 1_555 2.056 1.778 0.059 2.798 -7.854 178.595 3 A_CFL6:CFL12_B A 6 ? B 12 ? 15 2 1 A CFL 3 1_555 B CFL 3 1_555 2.107 1.873 0.009 1.040 6.526 177.806 4 A_CFL3:CFL9_B A 3 ? B 9 ? 15 2 1 A CFL 5 1_555 B CFL 5 1_555 2.048 1.860 0.149 -4.913 19.096 178.286 5 A_CFL5:CFL11_B A 5 ? B 11 ? 15 2 1 A CFL 4 1_555 B CFL 4 1_555 1.995 1.488 -0.101 12.960 -11.078 177.855 6 A_CFL4:CFL10_B A 4 ? B 10 ? 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 DT 1 1_555 B DT 1 1_555 A CFL 2 1_555 B CFL 2 1_555 -0.103 -0.062 2.586 2.607 -0.486 -148.750 0.034 -0.045 2.586 0.252 1.354 -148.759 1 AA_DT1CFL2:CFL8DT7_BB A 1 ? B 7 ? A 2 ? B 8 ? 1 A CFL 2 1_555 B CFL 2 1_555 A CFL 6 1_555 B CFL 6 1_555 2.188 -2.160 0.311 -126.964 -122.205 146.995 -1.051 -1.125 0.276 -61.156 63.538 178.927 2 AA_CFL2CFL6:CFL12CFL8_BB A 2 ? B 8 ? A 6 ? B 12 ? 1 A CFL 6 1_555 B CFL 6 1_555 A CFL 3 1_555 B CFL 3 1_555 -1.548 2.619 -0.057 -148.565 -99.004 73.840 1.279 0.820 -0.165 -49.665 74.526 178.826 3 AA_CFL6CFL3:CFL9CFL12_BB A 6 ? B 12 ? A 3 ? B 9 ? 1 A CFL 3 1_555 B CFL 3 1_555 A CFL 5 1_555 B CFL 5 1_555 -2.691 2.705 -0.099 133.895 118.652 -68.940 -1.357 -1.341 0.125 -59.484 67.126 -179.095 4 AA_CFL3CFL5:CFL11CFL9_BB A 3 ? B 9 ? A 5 ? B 11 ? 1 A CFL 5 1_555 B CFL 5 1_555 A CFL 4 1_555 B CFL 4 1_555 -2.005 2.219 0.290 -142.081 -105.395 59.070 1.228 0.843 0.394 -53.165 71.671 177.306 5 AA_CFL5CFL4:CFL10CFL11_BB A 5 ? B 11 ? A 4 ? B 10 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Spanish Ministry of Science, Innovation, and Universities' Spain PID2020-116620GB-I00 1 'H2020 Marie Curie Actions of the European Commission' 'European Union' 799693 2 # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 'NMR Distance Restraints' ? 2 1 'native gel electrophoresis' ? #