data_7BQD # _entry.id 7BQD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 7BQD pdb_00007bqd 10.2210/pdb7bqd/pdb WWPDB D_1300016038 ? ? BMRB 36333 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Solution NMR structure of NF8 (knot fold), de novo designed protein with a novel fold' _pdbx_database_related.db_id 36333 _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 7BQD _pdbx_database_status.recvd_initial_deposition_date 2020-03-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category CASD-NMR _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kobayashi, N.' 1 0000-0001-5136-2077 'Sugiki, T.' 2 0000-0003-1716-1241 'Fujiwara, T.' 3 ? 'Minami, S.' 4 0000-0001-9321-9279 'Koga, R.' 5 0000-0002-5068-1049 'Chikenji, G.' 6 ? 'Koga, N.' 7 0000-0001-8457-0809 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Nat.Struct.Mol.Biol. _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1545-9985 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Exploration of novel alpha-beta-protein folds through de novo design' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41594-023-01029-0 _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Minami, S.' 1 0000-0001-9321-9279 primary 'Kobayashi, N.' 2 0000-0001-5136-2077 primary 'Sugiki, T.' 3 0000-0003-1716-1241 primary 'Nagashima, T.' 4 0000-0003-0832-2066 primary 'Fujiwara, T.' 5 ? primary 'Koga, R.' 6 0000-0002-5068-1049 primary 'Chikenji, G.' 7 ? primary 'Koga, N.' 8 0000-0001-8457-0809 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description NF8 _entity.formula_weight 10296.638 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;GTILIFLDKNKEQAEKLAKEVGVTEIYESDNLEELYREIKERIERENPNATILTVTDPNELKKIQDEGKVDRIILLIKGS LEHHHHHH ; _entity_poly.pdbx_seq_one_letter_code_can ;GTILIFLDKNKEQAEKLAKEVGVTEIYESDNLEELYREIKERIERENPNATILTVTDPNELKKIQDEGKVDRIILLIKGS LEHHHHHH ; _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 GLY n 1 2 THR n 1 3 ILE n 1 4 LEU n 1 5 ILE n 1 6 PHE n 1 7 LEU n 1 8 ASP n 1 9 LYS n 1 10 ASN n 1 11 LYS n 1 12 GLU n 1 13 GLN n 1 14 ALA n 1 15 GLU n 1 16 LYS n 1 17 LEU n 1 18 ALA n 1 19 LYS n 1 20 GLU n 1 21 VAL n 1 22 GLY n 1 23 VAL n 1 24 THR n 1 25 GLU n 1 26 ILE n 1 27 TYR n 1 28 GLU n 1 29 SER n 1 30 ASP n 1 31 ASN n 1 32 LEU n 1 33 GLU n 1 34 GLU n 1 35 LEU n 1 36 TYR n 1 37 ARG n 1 38 GLU n 1 39 ILE n 1 40 LYS n 1 41 GLU n 1 42 ARG n 1 43 ILE n 1 44 GLU n 1 45 ARG n 1 46 GLU n 1 47 ASN n 1 48 PRO n 1 49 ASN n 1 50 ALA n 1 51 THR n 1 52 ILE n 1 53 LEU n 1 54 THR n 1 55 VAL n 1 56 THR n 1 57 ASP n 1 58 PRO n 1 59 ASN n 1 60 GLU n 1 61 LEU n 1 62 LYS n 1 63 LYS n 1 64 ILE n 1 65 GLN n 1 66 ASP n 1 67 GLU n 1 68 GLY n 1 69 LYS n 1 70 VAL n 1 71 ASP n 1 72 ARG n 1 73 ILE n 1 74 ILE n 1 75 LEU n 1 76 LEU n 1 77 ILE n 1 78 LYS n 1 79 GLY n 1 80 SER n 1 81 LEU n 1 82 GLU n 1 83 HIS n 1 84 HIS n 1 85 HIS n 1 86 HIS n 1 87 HIS n 1 88 HIS 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 88 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _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 'synthetic construct' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 32630 _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' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _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 ? _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7BQD _struct_ref.pdbx_db_accession 7BQD _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7BQD _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 88 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7BQD _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 88 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 88 # 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 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 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 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 aliphatic' 1 isotropic 3 1 1 '2D 1H-13C HSQC aromatic' 1 isotropic 4 1 1 '3D BEST-HNCO' 1 isotropic 5 1 1 '3D BEST-HNCACB' 1 isotropic 6 1 1 '3D BEST-HN(CO)CACB' 1 isotropic 7 1 1 '3D HCCH-TOCSY aliphatic' 1 isotropic 8 1 1 '3D HCCH-TOCSY aromatic' 1 isotropic 9 1 1 '3D 1H-15N NOESY' 1 isotropic 10 1 1 '3D 1H-13C NOESY aliphatic' 1 isotropic 11 1 1 '3D 1H-13C NOESY aromatic' 1 isotropic 12 1 1 '2D 1H-15N HSQC IPAP' 1 isotropic 13 1 2 '2D 1H-15N HSQC IPAP' 1 anisotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength 56.5 _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 NF8 _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 # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '0.95 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O' '95% H2O/5% D2O' NF8 solution ? 2 ;0.2 mM [U-100% 13C; U-100% 15N] NF8, 4.3 mM sodium phosphate, 5.7 mM potassium phosphate, 50 mM sodium chloride, 10 mg/mL Pf1 phage, 95% H2O/5% D2O ; '95% H2O/5% D2O' NF8_phage solution ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'AVANCE III' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 7BQD _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 8 # _pdbx_nmr_ensemble.entry_id 7BQD _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'target function' _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 7BQD _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'target function' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 collection TopSpin 3.2 'Bruker Biospin' 2 'peak picking' MAGRO 2.01.38 'Updated version of Kujira (Kobayashi, N. et al., 2007)' 3 processing NMRPipe 2017 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 4 'data analysis' NMRView 9.0 'Johnson, One Moon Scientific' 5 'chemical shift assignment' CYANA 3.98 'Guntert, Mumenthaler and Wuthrich' 6 'data analysis' TALOS 2017 'Cornilescu, Delaglio and Bax' 7 'structure calculation' CYANA 3.98 'Guntert, Mumenthaler and Wuthrich' 8 refinement Amber 12 '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 7BQD _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7BQD _struct.title 'Solution NMR structure of NF8 (knot fold); de novo designed protein with a novel fold' _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 7BQD _struct_keywords.text 'de novo designed protein, DE NOVO PROTEIN' _struct_keywords.pdbx_keywords 'DE NOVO 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 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 ASN A 10 ? GLY A 22 ? ASN A 10 GLY A 22 1 ? 13 HELX_P HELX_P2 AA2 ASN A 31 ? ASN A 47 ? ASN A 31 ASN A 47 1 ? 17 HELX_P HELX_P3 AA3 ASP A 57 ? GLY A 68 ? ASP A 57 GLY A 68 1 ? 12 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 4 _struct_sheet.details ? # 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 ? parallel AA1 2 3 ? parallel AA1 3 4 ? 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 ILE A 26 ? SER A 29 ? ILE A 26 SER A 29 AA1 2 ARG A 72 ? LYS A 78 ? ARG A 72 LYS A 78 AA1 3 THR A 2 ? ASP A 8 ? THR A 2 ASP A 8 AA1 4 THR A 51 ? VAL A 55 ? THR A 51 VAL A 55 # 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 TYR A 27 ? N TYR A 27 O LEU A 75 ? O LEU A 75 AA1 2 3 O LEU A 76 ? O LEU A 76 N PHE A 6 ? N PHE A 6 AA1 3 4 N ILE A 3 ? N ILE A 3 O THR A 51 ? O THR A 51 # _atom_sites.entry_id 7BQD _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 # 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 GLY 1 1 1 GLY GLY A . n A 1 2 THR 2 2 2 THR THR A . n A 1 3 ILE 3 3 3 ILE ILE A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 ILE 5 5 5 ILE ILE A . n A 1 6 PHE 6 6 6 PHE PHE A . n A 1 7 LEU 7 7 7 LEU LEU A . n A 1 8 ASP 8 8 8 ASP ASP A . n A 1 9 LYS 9 9 9 LYS LYS A . n A 1 10 ASN 10 10 10 ASN ASN A . n A 1 11 LYS 11 11 11 LYS LYS A . n A 1 12 GLU 12 12 12 GLU GLU A . n A 1 13 GLN 13 13 13 GLN GLN A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 GLU 15 15 15 GLU GLU A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 LEU 17 17 17 LEU LEU A . n A 1 18 ALA 18 18 18 ALA ALA A . n A 1 19 LYS 19 19 19 LYS LYS A . n A 1 20 GLU 20 20 20 GLU GLU A . n A 1 21 VAL 21 21 21 VAL VAL A . n A 1 22 GLY 22 22 22 GLY GLY A . n A 1 23 VAL 23 23 23 VAL VAL A . n A 1 24 THR 24 24 24 THR THR A . n A 1 25 GLU 25 25 25 GLU GLU A . n A 1 26 ILE 26 26 26 ILE ILE A . n A 1 27 TYR 27 27 27 TYR TYR A . n A 1 28 GLU 28 28 28 GLU GLU A . n A 1 29 SER 29 29 29 SER SER A . n A 1 30 ASP 30 30 30 ASP ASP A . n A 1 31 ASN 31 31 31 ASN ASN A . n A 1 32 LEU 32 32 32 LEU LEU A . n A 1 33 GLU 33 33 33 GLU GLU A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 LEU 35 35 35 LEU LEU A . n A 1 36 TYR 36 36 36 TYR TYR A . n A 1 37 ARG 37 37 37 ARG ARG A . n A 1 38 GLU 38 38 38 GLU GLU A . n A 1 39 ILE 39 39 39 ILE ILE A . n A 1 40 LYS 40 40 40 LYS LYS A . n A 1 41 GLU 41 41 41 GLU GLU A . n A 1 42 ARG 42 42 42 ARG ARG A . n A 1 43 ILE 43 43 43 ILE ILE A . n A 1 44 GLU 44 44 44 GLU GLU A . n A 1 45 ARG 45 45 45 ARG ARG A . n A 1 46 GLU 46 46 46 GLU GLU A . n A 1 47 ASN 47 47 47 ASN ASN A . n A 1 48 PRO 48 48 48 PRO PRO A . n A 1 49 ASN 49 49 49 ASN ASN A . n A 1 50 ALA 50 50 50 ALA ALA A . n A 1 51 THR 51 51 51 THR THR A . n A 1 52 ILE 52 52 52 ILE ILE A . n A 1 53 LEU 53 53 53 LEU LEU A . n A 1 54 THR 54 54 54 THR THR A . n A 1 55 VAL 55 55 55 VAL VAL A . n A 1 56 THR 56 56 56 THR THR A . n A 1 57 ASP 57 57 57 ASP ASP A . n A 1 58 PRO 58 58 58 PRO PRO A . n A 1 59 ASN 59 59 59 ASN ASN A . n A 1 60 GLU 60 60 60 GLU GLU A . n A 1 61 LEU 61 61 61 LEU LEU A . n A 1 62 LYS 62 62 62 LYS LYS A . n A 1 63 LYS 63 63 63 LYS LYS A . n A 1 64 ILE 64 64 64 ILE ILE A . n A 1 65 GLN 65 65 65 GLN GLN A . n A 1 66 ASP 66 66 66 ASP ASP A . n A 1 67 GLU 67 67 67 GLU GLU A . n A 1 68 GLY 68 68 68 GLY GLY A . n A 1 69 LYS 69 69 69 LYS LYS A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 ASP 71 71 71 ASP ASP A . n A 1 72 ARG 72 72 72 ARG ARG A . n A 1 73 ILE 73 73 73 ILE ILE A . n A 1 74 ILE 74 74 74 ILE ILE A . n A 1 75 LEU 75 75 75 LEU LEU A . n A 1 76 LEU 76 76 76 LEU LEU A . n A 1 77 ILE 77 77 77 ILE ILE A . n A 1 78 LYS 78 78 78 LYS LYS A . n A 1 79 GLY 79 79 79 GLY GLY A . n A 1 80 SER 80 80 80 SER SER A . n A 1 81 LEU 81 81 81 LEU LEU A . n A 1 82 GLU 82 82 82 GLU GLU A . n A 1 83 HIS 83 83 83 HIS HIS A . n A 1 84 HIS 84 84 84 HIS HIS A . n A 1 85 HIS 85 85 85 HIS HIS A . n A 1 86 HIS 86 86 86 HIS HIS A . n A 1 87 HIS 87 87 87 HIS HIS A . n A 1 88 HIS 88 88 88 HIS HIS A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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)' 6330 ? # _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 2021-03-24 2 'Structure model' 1 1 2023-06-14 3 'Structure model' 1 2 2023-07-05 # _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 2 'Structure model' Other 3 3 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' database_2 2 2 'Structure model' pdbx_database_status 3 3 'Structure model' citation # 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' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_citation.country' 5 3 'Structure model' '_citation.journal_abbrev' 6 3 'Structure model' '_citation.journal_id_CSD' 7 3 'Structure model' '_citation.journal_id_ISSN' 8 3 'Structure model' '_citation.pdbx_database_id_DOI' 9 3 'Structure model' '_citation.title' 10 3 'Structure model' '_citation.year' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 NF8 0.95 ? mM '[U-100% 13C; U-100% 15N]' 1 'sodium phosphate' 4.3 ? mM 'natural abundance' 1 'potassium phosphate' 5.7 ? mM 'natural abundance' 1 'sodium chloride' 50 ? mM 'natural abundance' 2 NF8 0.2 ? mM '[U-100% 13C; U-100% 15N]' 2 'sodium phosphate' 4.3 ? mM 'natural abundance' 2 'potassium phosphate' 5.7 ? mM 'natural abundance' 2 'sodium chloride' 50 ? mM 'natural abundance' 2 'Pf1 phage' 10 ? mg/mL 'natural abundance' # 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 NE A ARG 72 ? ? CZ A ARG 72 ? ? NH1 A ARG 72 ? ? 123.68 120.30 3.38 0.50 N 2 2 NE A ARG 45 ? ? CZ A ARG 45 ? ? NH1 A ARG 45 ? ? 123.52 120.30 3.22 0.50 N 3 4 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.84 120.30 3.54 0.50 N 4 6 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.57 120.30 3.27 0.50 N 5 7 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.64 120.30 3.34 0.50 N 6 8 NE A ARG 72 ? ? CZ A ARG 72 ? ? NH1 A ARG 72 ? ? 123.74 120.30 3.44 0.50 N 7 9 NE A ARG 45 ? ? CZ A ARG 45 ? ? NH1 A ARG 45 ? ? 123.50 120.30 3.20 0.50 N 8 10 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.67 120.30 3.37 0.50 N 9 12 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 124.76 120.30 4.46 0.50 N 10 13 NE A ARG 45 ? ? CZ A ARG 45 ? ? NH1 A ARG 45 ? ? 123.60 120.30 3.30 0.50 N 11 14 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.64 120.30 3.34 0.50 N 12 14 NE A ARG 42 ? ? CZ A ARG 42 ? ? NH1 A ARG 42 ? ? 123.87 120.30 3.57 0.50 N 13 15 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 124.71 120.30 4.41 0.50 N 14 15 NE A ARG 42 ? ? CZ A ARG 42 ? ? NH1 A ARG 42 ? ? 123.39 120.30 3.09 0.50 N 15 16 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.82 120.30 3.52 0.50 N 16 16 NE A ARG 72 ? ? CZ A ARG 72 ? ? NH1 A ARG 72 ? ? 123.60 120.30 3.30 0.50 N 17 17 NE A ARG 72 ? ? CZ A ARG 72 ? ? NH1 A ARG 72 ? ? 123.36 120.30 3.06 0.50 N 18 18 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 123.54 120.30 3.24 0.50 N 19 20 NE A ARG 37 ? ? CZ A ARG 37 ? ? NH1 A ARG 37 ? ? 124.56 120.30 4.26 0.50 N 20 20 NE A ARG 72 ? ? CZ A ARG 72 ? ? NH1 A ARG 72 ? ? 123.96 120.30 3.66 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 ASN A 31 ? ? -91.32 45.19 2 1 LYS A 69 ? ? -77.50 40.35 3 2 LYS A 69 ? ? -74.02 30.73 4 3 ASN A 31 ? ? -100.90 74.31 5 3 LYS A 69 ? ? -75.75 24.30 6 3 HIS A 83 ? ? -144.90 -33.72 7 3 HIS A 86 ? ? 52.57 71.59 8 4 HIS A 84 ? ? 57.24 167.32 9 5 HIS A 84 ? ? -143.13 21.17 10 5 HIS A 86 ? ? 59.50 -1.36 11 6 ASN A 10 ? ? -142.83 -11.13 12 6 LYS A 11 ? ? 64.02 -51.03 13 6 ASN A 31 ? ? -103.74 48.70 14 6 HIS A 85 ? ? 58.83 174.25 15 7 ASN A 31 ? ? -83.96 43.45 16 7 LYS A 69 ? ? -75.88 40.78 17 7 HIS A 83 ? ? 57.94 10.29 18 7 HIS A 86 ? ? 55.24 -171.43 19 8 ASN A 31 ? ? -90.45 53.76 20 9 ASN A 31 ? ? -93.31 44.32 21 9 HIS A 83 ? ? -146.19 -46.04 22 10 ASN A 31 ? ? -86.35 49.17 23 10 LYS A 69 ? ? -79.71 39.85 24 11 GLU A 12 ? ? 64.92 -44.20 25 11 ASN A 31 ? ? -81.02 49.01 26 11 LYS A 69 ? ? -71.98 35.52 27 12 LYS A 69 ? ? -80.30 43.95 28 12 HIS A 83 ? ? -148.92 -50.01 29 12 HIS A 86 ? ? 60.79 166.20 30 13 ASN A 31 ? ? -116.46 55.88 31 13 LYS A 69 ? ? -72.30 47.19 32 14 LYS A 69 ? ? -73.86 31.01 33 14 HIS A 85 ? ? -97.64 32.15 34 15 ASN A 31 ? ? -76.14 48.63 35 15 HIS A 86 ? ? 59.59 175.45 36 16 LYS A 69 ? ? -80.90 35.15 37 18 ASN A 31 ? ? -113.82 55.88 38 18 LYS A 69 ? ? -115.87 52.77 39 19 LYS A 69 ? ? -97.14 46.43 40 20 ASN A 31 ? ? -96.69 57.96 41 20 LYS A 69 ? ? -74.98 33.29 42 20 HIS A 83 ? ? -149.01 45.16 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan 18K06152 1 'Japan Agency for Medical Research and Development (AMED)' Japan JP19am0101072 2 'Japan Society for the Promotion of Science (JSPS)' Japan 18H05420 3 'Japan Society for the Promotion of Science (JSPS)' Japan 15H05592 4 'Japan Society for the Promotion of Science (JSPS)' Japan 19H03166 5 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details SEC-MALS #