data_7OMK # _entry.id 7OMK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 7OMK pdb_00007omk 10.2210/pdb7omk/pdb WWPDB D_1292113107 ? ? BMRB 34630 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'The NMR structure of the Zf-GRF domains from the mouse Endonuclease VIII-LIKE 3 (mNEIL3)' _pdbx_database_related.db_id 34630 _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 7OMK _pdbx_database_status.recvd_initial_deposition_date 2021-05-24 _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 REL _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 'Dinesh, D.C.' 1 0000-0001-9125-4775 'Huskova, A.' 2 0000-0001-9808-5660 'Srb, P.' 3 0000-0002-4562-578X 'Veverka, V.' 4 0000-0003-3782-5279 'Silhan, J.' 5 0000-0003-3868-5714 # _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 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 50 _citation.language ? _citation.page_first 10436 _citation.page_last 10448 _citation.title 'Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkac793 _citation.pdbx_database_id_PubMed 36155818 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huskova, A.' 1 ? primary 'Dinesh, D.C.' 2 ? primary 'Srb, P.' 3 ? primary 'Boura, E.' 4 ? primary 'Veverka, V.' 5 ? primary 'Silhan, J.' 6 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'Endonuclease 8-like 3' _entity.formula_weight 10818.668 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec 3.2.2.-,4.2.99.18 _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'DNA glycosylase FPG2,DNA glycosylase/AP lyase Neil3,Endonuclease VIII-like 3,Nei-like protein 3' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;SPLCKMHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADLSFPFCKHGKRSIMKTVLKIGPNNGKNFFVCPLEK EKQCNFFQWAENG ; _entity_poly.pdbx_seq_one_letter_code_can ;SPLCKMHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADLSFPFCKHGKRSIMKTVLKIGPNNGKNFFVCPLEK EKQCNFFQWAENG ; _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 SER n 1 2 PRO n 1 3 LEU n 1 4 CYS n 1 5 LYS n 1 6 MET n 1 7 HIS n 1 8 HIS n 1 9 ARG n 1 10 ARG n 1 11 CYS n 1 12 VAL n 1 13 LEU n 1 14 ARG n 1 15 VAL n 1 16 VAL n 1 17 ARG n 1 18 LYS n 1 19 ASP n 1 20 GLY n 1 21 GLU n 1 22 ASN n 1 23 LYS n 1 24 GLY n 1 25 ARG n 1 26 GLN n 1 27 PHE n 1 28 TYR n 1 29 ALA n 1 30 CYS n 1 31 SER n 1 32 LEU n 1 33 PRO n 1 34 ARG n 1 35 GLY n 1 36 ALA n 1 37 GLN n 1 38 CYS n 1 39 GLY n 1 40 PHE n 1 41 PHE n 1 42 GLU n 1 43 TRP n 1 44 ALA n 1 45 ASP n 1 46 LEU n 1 47 SER n 1 48 PHE n 1 49 PRO n 1 50 PHE n 1 51 CYS n 1 52 LYS n 1 53 HIS n 1 54 GLY n 1 55 LYS n 1 56 ARG n 1 57 SER n 1 58 ILE n 1 59 MET n 1 60 LYS n 1 61 THR n 1 62 VAL n 1 63 LEU n 1 64 LYS n 1 65 ILE n 1 66 GLY n 1 67 PRO n 1 68 ASN n 1 69 ASN n 1 70 GLY n 1 71 LYS n 1 72 ASN n 1 73 PHE n 1 74 PHE n 1 75 VAL n 1 76 CYS n 1 77 PRO n 1 78 LEU n 1 79 GLU n 1 80 LYS n 1 81 GLU n 1 82 LYS n 1 83 GLN n 1 84 CYS n 1 85 ASN n 1 86 PHE n 1 87 PHE n 1 88 GLN n 1 89 TRP n 1 90 ALA n 1 91 GLU n 1 92 ASN n 1 93 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 93 _entity_src_gen.gene_src_common_name Mouse _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Neil3 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 511693 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant STAR _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type 'Expression vector' _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details 'N-terminal His-SUMO tag ' _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pSUMO _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code NEIL3_MOUSE _struct_ref.pdbx_db_accession Q8K203 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;SPLCKMHHRRCVLRVVRKDGENKGRQFYACSLPRGAQCGFFEWADLSFPFCRHGKRSIMKTVLKIGPNNGKNFFVCPLEK KKQCNFFQWAENG ; _struct_ref.pdbx_align_begin 505 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7OMK _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 93 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q8K203 _struct_ref_seq.db_align_beg 505 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 597 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 505 _struct_ref_seq.pdbx_auth_seq_align_end 597 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 7OMK LYS A 52 ? UNP Q8K203 ARG 556 variant 556 1 1 7OMK GLU A 81 ? UNP Q8K203 LYS 585 variant 585 2 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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-15N HSQC' 1 isotropic 2 1 1 '2D 1H-13C HSQC' 1 isotropic 3 1 1 '3D HNCO' 1 isotropic 4 1 1 '3D HNCACB' 1 isotropic 5 1 1 '3D HBHA(CO)NH' 1 isotropic 6 1 1 '3D HN(CO)CA' 1 isotropic 9 1 1 '3D CBCA(CO)NH' 1 isotropic 8 1 1 '3D 1H-15N NOESY' 1 isotropic 7 1 1 '3D 1H-13C NOESY' 1 isotropic 11 1 1 '3D HCCH-TOCSY' 1 isotropic 10 1 1 '3D H(CCO)NH' 1 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.5 _pdbx_nmr_exptl_sample_conditions.ionic_strength 50 _pdbx_nmr_exptl_sample_conditions.details '250 uM [U-13C; U-15N] mNEIL3-GRF, 12.5 mM sodium phosphate, 50 mM sodium chloride, 1mM TCEP' _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label NMR_sample _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 '250 uM [U-13C; U-15N] NEIL3-GRF, 95% H2O/5% D2O' _pdbx_nmr_sample_details.solvent_system '95% H2O/5% D2O' _pdbx_nmr_sample_details.label 13C_15N _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details '250uM [U-13C; U-15N] mNEIL3-GRF, 12.5 mM sodium phosphate, 50 mM sodium chloride, 1mM TCEP' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 850 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 7OMK _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 3 # _pdbx_nmr_ensemble.entry_id 7OMK _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 35 _pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted' _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 7OMK _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'data analysis' TopSpin ? 'Bruker Biospin' 2 'data analysis' NMRFAM-SPARKY ? 'Lee W, Tonelli M, Markley JL' 3 'structure calculation' CYANA ? 'Guntert, Mumenthaler and Wuthrich' 4 'structure calculation' YASARA ? YASARA # _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 7OMK _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7OMK _struct.title 'The NMR structure of the Zf-GRF domains from the mouse Endonuclease VIII-LIKE 3 (mNEIL3)' _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 7OMK _struct_keywords.text 'Zinc Finger, NEIL3-GRF, DNA repair, DNA damage, DNA BINDING PROTEIN' _struct_keywords.pdbx_keywords 'DNA BINDING PROTEIN' # _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_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id ASP _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 45 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id PHE _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 48 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ASP _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 549 _struct_conf.end_auth_comp_id PHE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 552 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 4 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA1 2 3 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL A 12 ? VAL A 15 ? VAL A 516 VAL A 519 AA1 2 GLN A 26 ? ALA A 29 ? GLN A 530 ALA A 533 AA1 3 GLU A 42 ? TRP A 43 ? GLU A 546 TRP A 547 AA2 1 ILE A 58 ? THR A 61 ? ILE A 562 THR A 565 AA2 2 ASN A 72 ? VAL A 75 ? ASN A 576 VAL A 579 AA2 3 GLN A 88 ? TRP A 89 ? GLN A 592 TRP A 593 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N ARG A 14 ? N ARG A 518 O PHE A 27 ? O PHE A 531 AA1 2 3 N TYR A 28 ? N TYR A 532 O GLU A 42 ? O GLU A 546 AA2 1 2 N ILE A 58 ? N ILE A 562 O VAL A 75 ? O VAL A 579 AA2 2 3 N PHE A 74 ? N PHE A 578 O GLN A 88 ? O GLN A 592 # _atom_sites.entry_id 7OMK _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 H N O S # 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 SER 1 505 505 SER SER A . n A 1 2 PRO 2 506 506 PRO PRO A . n A 1 3 LEU 3 507 507 LEU LEU A . n A 1 4 CYS 4 508 508 CYS CYS A . n A 1 5 LYS 5 509 509 LYS LYS A . n A 1 6 MET 6 510 510 MET MET A . n A 1 7 HIS 7 511 511 HIS HIS A . n A 1 8 HIS 8 512 512 HIS HIS A . n A 1 9 ARG 9 513 513 ARG ARG A . n A 1 10 ARG 10 514 514 ARG ARG A . n A 1 11 CYS 11 515 515 CYS CYS A . n A 1 12 VAL 12 516 516 VAL VAL A . n A 1 13 LEU 13 517 517 LEU LEU A . n A 1 14 ARG 14 518 518 ARG ARG A . n A 1 15 VAL 15 519 519 VAL VAL A . n A 1 16 VAL 16 520 520 VAL VAL A . n A 1 17 ARG 17 521 521 ARG ARG A . n A 1 18 LYS 18 522 522 LYS LYS A . n A 1 19 ASP 19 523 523 ASP ASP A . n A 1 20 GLY 20 524 524 GLY GLY A . n A 1 21 GLU 21 525 525 GLU GLU A . n A 1 22 ASN 22 526 526 ASN ASN A . n A 1 23 LYS 23 527 527 LYS LYS A . n A 1 24 GLY 24 528 528 GLY GLY A . n A 1 25 ARG 25 529 529 ARG ARG A . n A 1 26 GLN 26 530 530 GLN GLN A . n A 1 27 PHE 27 531 531 PHE PHE A . n A 1 28 TYR 28 532 532 TYR TYR A . n A 1 29 ALA 29 533 533 ALA ALA A . n A 1 30 CYS 30 534 534 CYS CYS A . n A 1 31 SER 31 535 535 SER SER A . n A 1 32 LEU 32 536 536 LEU LEU A . n A 1 33 PRO 33 537 537 PRO PRO A . n A 1 34 ARG 34 538 538 ARG ARG A . n A 1 35 GLY 35 539 539 GLY GLY A . n A 1 36 ALA 36 540 540 ALA ALA A . n A 1 37 GLN 37 541 541 GLN GLN A . n A 1 38 CYS 38 542 542 CYS CYS A . n A 1 39 GLY 39 543 543 GLY GLY A . n A 1 40 PHE 40 544 544 PHE PHE A . n A 1 41 PHE 41 545 545 PHE PHE A . n A 1 42 GLU 42 546 546 GLU GLU A . n A 1 43 TRP 43 547 547 TRP TRP A . n A 1 44 ALA 44 548 548 ALA ALA A . n A 1 45 ASP 45 549 549 ASP ASP A . n A 1 46 LEU 46 550 550 LEU LEU A . n A 1 47 SER 47 551 551 SER SER A . n A 1 48 PHE 48 552 552 PHE PHE A . n A 1 49 PRO 49 553 553 PRO PRO A . n A 1 50 PHE 50 554 554 PHE PHE A . n A 1 51 CYS 51 555 555 CYS CYS A . n A 1 52 LYS 52 556 556 LYS LYS A . n A 1 53 HIS 53 557 557 HIS HIS A . n A 1 54 GLY 54 558 558 GLY GLY A . n A 1 55 LYS 55 559 559 LYS LYS A . n A 1 56 ARG 56 560 560 ARG ARG A . n A 1 57 SER 57 561 561 SER SER A . n A 1 58 ILE 58 562 562 ILE ILE A . n A 1 59 MET 59 563 563 MET MET A . n A 1 60 LYS 60 564 564 LYS LYS A . n A 1 61 THR 61 565 565 THR THR A . n A 1 62 VAL 62 566 566 VAL VAL A . n A 1 63 LEU 63 567 567 LEU LEU A . n A 1 64 LYS 64 568 568 LYS LYS A . n A 1 65 ILE 65 569 569 ILE ILE A . n A 1 66 GLY 66 570 570 GLY GLY A . n A 1 67 PRO 67 571 571 PRO PRO A . n A 1 68 ASN 68 572 572 ASN ASN A . n A 1 69 ASN 69 573 573 ASN ASN A . n A 1 70 GLY 70 574 574 GLY GLY A . n A 1 71 LYS 71 575 575 LYS LYS A . n A 1 72 ASN 72 576 576 ASN ASN A . n A 1 73 PHE 73 577 577 PHE PHE A . n A 1 74 PHE 74 578 578 PHE PHE A . n A 1 75 VAL 75 579 579 VAL VAL A . n A 1 76 CYS 76 580 580 CYS CYS A . n A 1 77 PRO 77 581 581 PRO PRO A . n A 1 78 LEU 78 582 582 LEU LEU A . n A 1 79 GLU 79 583 583 GLU GLU A . n A 1 80 LYS 80 584 584 LYS LYS A . n A 1 81 GLU 81 585 585 GLU GLU A . n A 1 82 LYS 82 586 586 LYS LYS A . n A 1 83 GLN 83 587 587 GLN GLN A . n A 1 84 CYS 84 588 588 CYS CYS A . n A 1 85 ASN 85 589 589 ASN ASN A . n A 1 86 PHE 86 590 590 PHE PHE A . n A 1 87 PHE 87 591 591 PHE PHE A . n A 1 88 GLN 88 592 592 GLN GLN A . n A 1 89 TRP 89 593 593 TRP TRP A . n A 1 90 ALA 90 594 594 ALA ALA A . n A 1 91 GLU 91 595 595 GLU GLU A . n A 1 92 ASN 92 596 596 ASN ASN A . n A 1 93 GLY 93 597 597 GLY GLY A . n # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # 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)' 7110 ? # _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_ _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 2022-06-01 2 'Structure model' 1 1 2022-10-19 3 'Structure model' 1 2 2022-10-26 4 'Structure model' 1 3 2023-06-14 # _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' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' Other # 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' citation 4 3 'Structure model' citation_author 5 4 'Structure model' pdbx_database_status # 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_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 3 'Structure model' '_citation.journal_volume' 11 3 'Structure model' '_citation.page_first' 12 3 'Structure model' '_citation.page_last' 13 3 'Structure model' '_citation_author.identifier_ORCID' 14 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component NEIL3-GRF _pdbx_nmr_exptl_sample.concentration 250 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units uM _pdbx_nmr_exptl_sample.isotopic_labeling '[U-13C; U-15N]' # 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 5 NE A ARG 514 ? ? CZ A ARG 514 ? ? NH1 A ARG 514 ? ? 123.71 120.30 3.41 0.50 N 2 10 NE A ARG 514 ? ? CZ A ARG 514 ? ? NH1 A ARG 514 ? ? 123.59 120.30 3.29 0.50 N 3 29 NE A ARG 529 ? ? CZ A ARG 529 ? ? NH1 A ARG 529 ? ? 123.37 120.30 3.07 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 CYS A 515 ? ? -123.22 -59.58 2 2 CYS A 515 ? ? -124.15 -59.74 3 2 GLU A 595 ? ? -129.86 -74.56 4 3 SER A 535 ? ? -141.46 36.27 5 4 GLN A 541 ? ? 179.19 172.45 6 4 GLU A 595 ? ? 26.70 55.81 7 5 SER A 535 ? ? -142.94 34.94 8 5 PRO A 553 ? ? -78.03 -104.72 9 6 CYS A 515 ? ? -124.01 -59.74 10 7 CYS A 515 ? ? -124.07 -54.80 11 7 ASP A 523 ? ? 65.02 -162.38 12 7 GLU A 595 ? ? 53.19 86.56 13 8 CYS A 515 ? ? -124.21 -56.18 14 8 GLU A 595 ? ? 57.94 -136.57 15 9 CYS A 515 ? ? -123.89 -58.42 16 9 ASN A 596 ? ? -141.31 21.98 17 10 CYS A 515 ? ? -124.07 -56.65 18 12 CYS A 515 ? ? -123.61 -55.47 19 13 CYS A 515 ? ? -123.96 -59.71 20 13 ASP A 523 ? ? 63.70 -178.68 21 14 CYS A 515 ? ? -124.04 -55.26 22 15 ASP A 523 ? ? -179.65 -160.01 23 16 CYS A 515 ? ? -124.15 -59.12 24 16 ASP A 523 ? ? 62.64 -159.32 25 16 ASN A 589 ? ? -72.72 21.51 26 16 GLU A 595 ? ? 72.63 -29.13 27 17 CYS A 515 ? ? -124.23 -54.66 28 17 ASP A 523 ? ? 176.09 -160.41 29 18 CYS A 515 ? ? -124.05 -54.67 30 19 CYS A 515 ? ? -123.58 -54.94 31 19 ASN A 596 ? ? -152.05 -0.81 32 21 CYS A 515 ? ? -123.98 -55.07 33 21 LYS A 522 ? ? -100.07 -166.57 34 21 ASP A 523 ? ? 61.33 -161.56 35 21 GLU A 595 ? ? 44.79 -34.47 36 21 ASN A 596 ? ? -143.41 -0.93 37 22 CYS A 515 ? ? -124.06 -55.14 38 23 CYS A 515 ? ? -123.88 -54.91 39 23 GLU A 595 ? ? 38.24 53.59 40 24 CYS A 515 ? ? -124.14 -54.68 41 24 GLN A 541 ? ? -176.41 -179.43 42 25 CYS A 515 ? ? -123.75 -55.04 43 25 GLU A 595 ? ? 59.20 0.02 44 26 CYS A 515 ? ? -124.16 -59.71 45 26 GLU A 595 ? ? 59.13 -157.81 46 27 GLN A 541 ? ? -176.73 -179.41 47 27 PRO A 553 ? ? -88.05 -142.81 48 27 GLU A 595 ? ? 57.47 -161.66 49 28 CYS A 515 ? ? -123.98 -59.66 50 28 ASP A 523 ? ? 62.76 -164.71 51 28 ASN A 589 ? ? -78.54 34.64 52 28 ASN A 596 ? ? -147.37 -39.67 53 30 GLU A 595 ? ? 57.92 -91.68 54 30 ASN A 596 ? ? -148.29 22.50 55 31 CYS A 515 ? ? -123.96 -56.32 56 31 ASP A 523 ? ? 60.31 -157.03 57 33 CYS A 515 ? ? -123.80 -55.12 58 33 ARG A 521 ? ? -91.07 32.80 59 33 GLU A 595 ? ? -130.93 -102.26 60 34 CYS A 515 ? ? -122.18 -55.10 61 34 LYS A 522 ? ? -78.77 -169.64 62 34 ASP A 523 ? ? 58.70 -167.85 63 34 ASN A 596 ? ? -95.28 55.19 64 35 CYS A 515 ? ? -124.07 -59.82 65 35 ASN A 596 ? ? -144.09 22.80 # _pdbx_audit_support.funding_organization 'Czech Academy of Sciences' _pdbx_audit_support.country 'Czech Republic' _pdbx_audit_support.grant_number 'RVO: 61388963' _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #