data_6VGT # _entry.id 6VGT # _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 6VGT pdb_00006vgt 10.2210/pdb6vgt/pdb WWPDB D_1000246368 ? ? BMRB 30710 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details ;Solution NMR structure of enterococcal cytolysin L (CylLL") produced by Enterococcus faecalis ; _pdbx_database_related.db_id 30710 _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 6VGT _pdbx_database_status.recvd_initial_deposition_date 2020-01-08 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Bobeica, S.C.' 1 0000-0001-5058-5543 'van der Donk, W.A.' 2 0000-0002-5467-7071 'Zhu, L.' 3 0000-0002-6657-271X 'Tang, W.' 4 0000-0002-5739-5416 # loop_ _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 _citation.database_id_Medline _citation.details _citation.id _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_full _citation.journal_issue _citation.journal_volume _citation.language _citation.page_first _citation.page_last _citation.title _citation.year _citation.database_id_CSD _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.unpublished_flag ? ? ? ? ? ? ? UK ? ? primary 'Chem Sci' ? ? 2041-6520 ? ? 11 ? 12854 12870 'Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.' 2020 ? 10.1039/d0sc01651a 34094481 ? ? ? ? ? ? ? ? UK ? ? 1 'Chem Sci' ? ? 2041-6520 ? ? 11 ? 12871 12876 'Correction: Structural determinants of macrocyclization in substrate-controlled lanthipeptide biosynthetic pathways.' 2020 ? 10.1039/d0sc90208j 34101773 ? ? ? ? ? ? ? ? US ? ? 2 Nat.Chem.Biol. ? ? 1552-4469 ? ? 9 ? 157 159 'The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry.' 2013 ? 10.1038/nchembio.1162 23314913 ? ? ? ? ? ? ? ? US ? ? 3 Nat.Chem.Biol. ? ? 1552-4469 ? ? 9 ? 157 159 'The sequence of the enterococcal cytolysin imparts unusual lanthionine stereochemistry.' 2013 ? 10.1038/nchembio.1162 23314913 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Bobeica, S.C.' 1 0000-0001-5058-5543 primary 'Zhu, L.' 2 0000-0002-6657-271X primary 'Acedo, J.Z.' 3 0000-0002-6648-770X primary 'Tang, W.' 4 0000-0002-5739-5416 primary 'van der Donk, W.A.' 5 0000-0002-5467-7071 1 'Bobeica, S.C.' 6 0000-0001-5058-5543 1 'Zhu, L.' 7 0000-0002-6657-271X 1 'Acedo, J.Z.' 8 0000-0002-6648-770X 1 'Tang, W.' 9 0000-0002-5739-5416 1 'van der Donk, W.A.' 10 0000-0002-5467-7071 2 'Tang, W.' 11 ? 2 'van der Donk, W.A.' 12 ? 3 'Tang, W.' 13 ? 3 'van der Donk, W.A.' 14 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'cytolysin L' _entity.formula_weight 3446.074 _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 yes _entity_poly.pdbx_seq_one_letter_code '(ABA)(DBU)PVCAVAA(DBU)AAAA(DHA)AACGWVGGGIFTGV(DBU)VVV(DAL)LKHC' _entity_poly.pdbx_seq_one_letter_code_can ATPVCAVAATAAAASAACGWVGGGIFTGVTVVVALKHC _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 ABA n 1 2 DBU n 1 3 PRO n 1 4 VAL n 1 5 CYS n 1 6 ALA n 1 7 VAL n 1 8 ALA n 1 9 ALA n 1 10 DBU n 1 11 ALA n 1 12 ALA n 1 13 ALA n 1 14 ALA n 1 15 DHA n 1 16 ALA n 1 17 ALA n 1 18 CYS n 1 19 GLY n 1 20 TRP n 1 21 VAL n 1 22 GLY n 1 23 GLY n 1 24 GLY n 1 25 ILE n 1 26 PHE n 1 27 THR n 1 28 GLY n 1 29 VAL n 1 30 DBU n 1 31 VAL n 1 32 VAL n 1 33 VAL n 1 34 DAL n 1 35 LEU n 1 36 LYS n 1 37 HIS n 1 38 CYS 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 38 _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 'Enterococcus faecalis' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1351 _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 6VGT _struct_ref.pdbx_db_accession 6VGT _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 6VGT _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 38 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6VGT _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 38 _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 38 # 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 ABA 'L-peptide linking' n 'ALPHA-AMINOBUTYRIC ACID' ? 'C4 H9 N O2' 103.120 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DAL 'D-peptide linking' . D-ALANINE ? 'C3 H7 N O2' 89.093 DBU 'peptide linking' n '(2Z)-2-AMINOBUT-2-ENOIC ACID' Z-DEHYDROBUTYRINE 'C4 H7 N O2' 101.104 DHA 'peptide linking' n '2-AMINO-ACRYLIC ACID' 2,3-DIDEHYDROALANINE 'C3 H5 N O2' 87.077 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 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 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-1H TOCSY' 1 isotropic 2 1 1 '2D 1H-1H NOESY' 1 isotropic # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 296 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 6 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err 0 _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined' _pdbx_nmr_exptl_sample_conditions.label 'CylLL"_details' _pdbx_nmr_exptl_sample_conditions.pH_err 0.1 _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err 0 _pdbx_nmr_exptl_sample_conditions.temperature_err 0.1 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2.0 mM cytolysin L, methanol' _pdbx_nmr_sample_details.solvent_system methanol _pdbx_nmr_sample_details.label 'CylLL"' _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details 'CD3-OH with DSS standard' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 6VGT _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 6 # _pdbx_nmr_ensemble.entry_id 6VGT _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _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 6VGT _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria medoid # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'data analysis' Sparky ? Goddard 2 'data analysis' NMRDraw ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 3 processing NMRPipe ? 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 4 'chemical shift assignment' Sparky ? Goddard 5 'peak picking' Sparky ? Goddard 6 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 7 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' # _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 6VGT _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6VGT _struct.title ;Solution NMR structure of enterococcal cytolysin L (CylLL") produced by Enterococcus faecalis ; _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 6VGT _struct_keywords.text 'lanthipeptide, cytolysin, cyclic peptide, posttranslational modification, TOXIN' _struct_keywords.pdbx_keywords TOXIN # _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 ABA A 1 ? VAL A 21 ? ABA A 1 VAL A 21 1 ? 21 HELX_P HELX_P2 AA2 GLY A 23 ? CYS A 38 ? GLY A 23 CYS A 38 1 ? 16 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 ABA 1 C ? ? ? 1_555 A DBU 2 N ? ? A ABA 1 A DBU 2 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale2 covale none ? A ABA 1 CB ? ? ? 1_555 A CYS 5 SG ? ? A ABA 1 A CYS 5 1_555 ? ? ? ? ? ? ? 1.810 ? ? covale3 covale both ? A DBU 2 C ? ? ? 1_555 A PRO 3 N ? ? A DBU 2 A PRO 3 1_555 ? ? ? ? ? ? ? 1.306 ? ? covale4 covale both ? A ALA 9 C ? ? ? 1_555 A DBU 10 N ? ? A ALA 9 A DBU 10 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale5 covale both ? A DBU 10 C ? ? ? 1_555 A ALA 11 N ? ? A DBU 10 A ALA 11 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale6 covale both ? A ALA 14 C ? ? ? 1_555 A DHA 15 N ? ? A ALA 14 A DHA 15 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale7 covale both ? A DHA 15 C ? ? ? 1_555 A ALA 16 N ? ? A DHA 15 A ALA 16 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale8 covale both ? A VAL 29 C ? ? ? 1_555 A DBU 30 N ? ? A VAL 29 A DBU 30 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale9 covale both ? A DBU 30 C ? ? ? 1_555 A VAL 31 N ? ? A DBU 30 A VAL 31 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale10 covale both ? A VAL 33 C ? ? ? 1_555 A DAL 34 N ? ? A VAL 33 A DAL 34 1_555 ? ? ? ? ? ? ? 1.316 ? ? covale11 covale both ? A DAL 34 C ? ? ? 1_555 A LEU 35 N ? ? A DAL 34 A LEU 35 1_555 ? ? ? ? ? ? ? 1.327 ? ? covale12 covale none ? A DAL 34 CB ? ? ? 1_555 A CYS 38 SG ? ? A DAL 34 A CYS 38 1_555 ? ? ? ? ? ? ? 1.815 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6VGT _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 ABA 1 1 1 ABA ABU A . n A 1 2 DBU 2 2 2 DBU DHB A . n A 1 3 PRO 3 3 3 PRO PRO A . n A 1 4 VAL 4 4 4 VAL VAL A . n A 1 5 CYS 5 5 5 CYS CYS A . n A 1 6 ALA 6 6 6 ALA ALA A . n A 1 7 VAL 7 7 7 VAL VAL A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 ALA 9 9 9 ALA ALA A . n A 1 10 DBU 10 10 10 DBU DHB A . n A 1 11 ALA 11 11 11 ALA ALA A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 ALA 13 13 13 ALA ALA A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 DHA 15 15 15 DHA DHA A . n A 1 16 ALA 16 16 16 ALA ALA A . n A 1 17 ALA 17 17 17 ALA ALA A . n A 1 18 CYS 18 18 18 CYS CYS A . n A 1 19 GLY 19 19 19 GLY GLY A . n A 1 20 TRP 20 20 20 TRP TRP 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 GLY 23 23 23 GLY GLY A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 ILE 25 25 25 ILE ILE A . n A 1 26 PHE 26 26 26 PHE PHE A . n A 1 27 THR 27 27 27 THR THR A . n A 1 28 GLY 28 28 28 GLY GLY A . n A 1 29 VAL 29 29 29 VAL VAL A . n A 1 30 DBU 30 30 30 DBU DHB A . n A 1 31 VAL 31 31 31 VAL VAL A . n A 1 32 VAL 32 32 32 VAL VAL A . n A 1 33 VAL 33 33 33 VAL VAL A . n A 1 34 DAL 34 34 34 DAL DAL A . n A 1 35 LEU 35 35 35 LEU LEU A . n A 1 36 LYS 36 36 36 LYS LYS A . n A 1 37 HIS 37 37 37 HIS HIS A . n A 1 38 CYS 38 38 38 CYS CYS 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 # _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 2020-07-08 2 'Structure model' 2 0 2020-09-09 3 'Structure model' 2 1 2021-07-14 4 'Structure model' 2 2 2023-06-14 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 2 'Structure model' author 'Coordinate replacement' 'Chirality error' ;Residue ABA 1 should have been (R) configuration at CB. An additional improper angle was defined in the XPLOR patch command to ensure (R) configuration at CB of ABA in LL (methyl) lanthionine linkages is maintained. ; # 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' Advisory 2 2 'Structure model' 'Atomic model' 3 2 'Structure model' 'Author supporting evidence' 4 2 'Structure model' 'Data collection' 5 2 'Structure model' 'Derived calculations' 6 2 'Structure model' 'Refinement description' 7 2 'Structure model' 'Structure summary' 8 3 'Structure model' 'Database references' 9 4 'Structure model' 'Database references' 10 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' atom_site 2 2 'Structure model' entity_name_com 3 2 'Structure model' pdbx_entity_instance_feature 4 2 'Structure model' pdbx_nmr_refine 5 2 'Structure model' pdbx_nmr_representative 6 2 'Structure model' pdbx_struct_assembly 7 2 'Structure model' pdbx_validate_close_contact 8 2 'Structure model' pdbx_validate_torsion 9 2 'Structure model' struct_conn 10 3 'Structure model' citation 11 3 'Structure model' citation_author 12 4 'Structure model' database_2 13 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' '_atom_site.Cartn_x' 2 2 'Structure model' '_atom_site.Cartn_y' 3 2 'Structure model' '_atom_site.Cartn_z' 4 2 'Structure model' '_pdbx_nmr_refine.software_ordinal' 5 2 'Structure model' '_pdbx_nmr_representative.selection_criteria' 6 2 'Structure model' '_pdbx_struct_assembly.details' 7 2 'Structure model' '_pdbx_struct_assembly.method_details' 8 2 'Structure model' '_struct_conn.pdbx_dist_value' 9 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 10 2 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 2 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 2 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 2 'Structure model' '_struct_conn.ptnr2_label_atom_id' 14 2 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 2 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 4 'Structure model' '_database_2.pdbx_DOI' 17 4 'Structure model' '_database_2.pdbx_database_accession' 18 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' # _pdbx_entry_details.entry_id 6VGT _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component 'cytolysin L' _pdbx_nmr_exptl_sample.concentration 2.0 _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 1 O A ABA 1 ? ? H A CYS 5 ? ? 1.48 2 1 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 3 2 O A DAL 34 ? ? H A CYS 38 ? ? 1.55 4 2 O A ABA 1 ? ? H A CYS 5 ? ? 1.56 5 2 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 6 3 O A ABA 1 ? ? H A CYS 5 ? ? 1.48 7 3 O A DAL 34 ? ? H A CYS 38 ? ? 1.54 8 3 O A ALA 17 ? ? H A VAL 21 ? ? 1.58 9 3 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 10 4 O A DAL 34 ? ? H A CYS 38 ? ? 1.53 11 4 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 12 5 O A DAL 34 ? ? H A CYS 38 ? ? 1.47 13 5 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 14 6 O A ABA 1 ? ? H A CYS 5 ? ? 1.53 15 6 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 16 7 O A DAL 34 ? ? H A CYS 38 ? ? 1.47 17 7 O A ABA 1 ? ? H A CYS 5 ? ? 1.55 18 7 O A GLY 24 ? ? H A PHE 26 ? ? 1.58 19 7 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 20 8 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 21 9 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 22 9 O A DAL 34 ? ? N A CYS 38 ? ? 2.19 23 10 O A ABA 1 ? ? H A CYS 5 ? ? 1.49 24 10 O A VAL 32 ? ? H A LYS 36 ? ? 1.54 25 10 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 26 11 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 27 12 O A ABA 1 ? ? H A CYS 5 ? ? 1.55 28 12 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 29 13 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 30 14 O A VAL 33 ? ? H A HIS 37 ? ? 1.50 31 14 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 32 15 O A ABA 1 ? ? H A CYS 5 ? ? 1.51 33 15 O A VAL 33 ? ? H A HIS 37 ? ? 1.59 34 15 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 35 16 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 36 17 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 37 18 O A VAL 32 ? ? H A LYS 36 ? ? 1.58 38 18 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 39 19 O A ABA 1 ? ? H A CYS 5 ? ? 1.58 40 19 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 41 20 O A DAL 34 ? ? H A CYS 38 ? ? 1.58 42 20 CB A ALA 14 ? ? SG A CYS 18 ? ? 1.81 # 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 DAL A 34 ? ? -44.46 -84.38 2 3 VAL A 21 ? ? 26.77 73.43 3 5 ALA A 17 ? ? -74.61 -71.96 4 5 TRP A 20 ? ? -80.63 -79.81 5 5 VAL A 21 ? ? -56.26 -87.89 6 5 LEU A 35 ? ? -48.04 -15.29 7 6 VAL A 21 ? ? -36.59 -75.53 8 6 HIS A 37 ? ? -143.65 -62.81 9 7 VAL A 21 ? ? 18.07 -85.05 10 7 ILE A 25 ? ? 68.30 -49.88 11 7 LEU A 35 ? ? -46.71 -18.60 12 8 VAL A 21 ? ? 38.41 22.55 13 9 ALA A 17 ? ? -78.27 -70.49 14 9 VAL A 21 ? ? 30.05 -147.13 15 9 HIS A 37 ? ? -146.50 -62.73 16 10 VAL A 33 ? ? -50.65 -73.06 17 10 DAL A 34 ? ? -35.12 -62.25 18 10 HIS A 37 ? ? -128.35 -54.36 19 11 VAL A 21 ? ? -91.87 -157.48 20 11 HIS A 37 ? ? -150.47 -107.36 21 12 VAL A 21 ? ? 22.76 -135.02 22 12 ILE A 25 ? ? -34.62 -30.02 23 12 HIS A 37 ? ? -115.75 -83.08 24 14 VAL A 21 ? ? 34.61 27.67 25 14 VAL A 33 ? ? -50.88 -70.40 26 14 HIS A 37 ? ? 161.21 101.36 27 15 ILE A 25 ? ? 69.77 -51.54 28 15 HIS A 37 ? ? 160.38 107.75 29 16 VAL A 4 ? ? -63.87 -71.41 30 16 VAL A 21 ? ? 27.36 41.39 31 16 ILE A 25 ? ? -34.13 -28.73 32 17 HIS A 37 ? ? 162.17 105.46 33 18 ILE A 25 ? ? -34.68 -28.60 34 18 HIS A 37 ? ? -112.94 -91.18 35 19 VAL A 21 ? ? 69.30 -61.07 36 19 HIS A 37 ? ? 161.86 104.78 37 20 VAL A 21 ? ? 37.29 59.31 38 20 ILE A 25 ? ? 70.25 -49.55 # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number R37GM058822 _pdbx_audit_support.ordinal 1 # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 ABA ? ? ABA ? ? 'SUBJECT OF INVESTIGATION' ? 2 DAL ? ? DAL ? ? 'SUBJECT OF INVESTIGATION' ? 3 DHA ? ? DHA ? ? 'SUBJECT OF INVESTIGATION' ? 4 DBU ? ? DBU ? ? 'SUBJECT OF INVESTIGATION' ? # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'mass spectrometry' _pdbx_struct_assembly_auth_evidence.details ? #