data_6QYW # _entry.id 6QYW # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.315 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 6QYW WWPDB D_1292101156 BMRB 34374 # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB . 1WCO unspecified PDB 'solution nmr of synthetic Nisin Ring B (Lan8,11) analogue' 6QM1 unspecified PDB 'solution nmr of synthetic Mutacin I Ring B, major conformer' 6QTF unspecified PDB 'solution nmr of synthetic Mutacin I Ring B, minor conformer' 6QYR unspecified PDB 'solution nmr of synthetic nisin ring B' 6QYS unspecified PDB 'solution nmr of synthetic Mutacin I Ring A (Ser2, Ala5, Ala8) analogue' 6QYV unspecified PDB 'solution nmr of synthetic Mutacin I Ring A truncated analogue' 6QYT unspecified PDB 'solution nmr of synthetic mutacin I ring A' 6QYU unspecified BMRB 'Solution NMR of synthetic analogues of nisin and mutacin ring A and ring B - nisin ring A' 34374 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 6QYW _pdbx_database_status.recvd_initial_deposition_date 2019-03-09 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Dickman, R.' 1 0000-0003-3139-5423 'Mitchell, S.A.' 2 ? 'Figueiredo, A.' 3 0000-0001-7039-5341 'Hansen, D.F.' 4 0000-0003-0891-220X 'Tabor, A.B.' 5 0000-0001-8216-0347 # 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 ? ? ? ? ? ? ? US ? ? primary J.Org.Chem. JOCEAH 0035 0022-3263 ? ? 84 ? 11493 11512 ;Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B. ; 2019 ? 10.1021/acs.joc.9b01253 31464129 ? ? ? ? ? ? ? ? ? ? ? 1 'To Be Published' ? 0353 ? ? ? ? ? ? ? ;A chemical biology approach to understanding molecular recognition of lipid II by nisin: Solid-phase synthesis and NMR ensemble analysis of nisin(1-12) and a synthetic ana-logue. ; ? ? ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dickman, R.' 1 ? primary 'Mitchell, S.A.' 2 ? primary 'Figueiredo, A.M.' 3 ? primary 'Hansen, D.F.' 4 ? primary 'Tabor, A.B.' 5 ? 1 'Dickman, R.' 6 0000-0003-3139-5423 1 'Danelius, E.' 7 0000-0002-7322-9661 1 'Mitchell, S.A.' 8 ? 1 'Hansen, D.F.' 9 0000-0003-0891-220X 1 'Erdelyi, M.' 10 0000-0003-0359-5970 1 'Tabor, A.B.' 11 0000-0001-8216-0347 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ILE-DBU-DAL-ILE-DHA-LEU-CYS-ALA _entity.formula_weight 754.938 _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 'I(DBU)(DAL)I(DHA)LCA' _entity_poly.pdbx_seq_one_letter_code_can ITAISLCA _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 ILE n 1 2 DBU n 1 3 DAL n 1 4 ILE n 1 5 DHA n 1 6 LEU n 1 7 CYS n 1 8 ALA 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 8 _pdbx_entity_src_syn.organism_scientific 'Lactococcus lactis' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 1358 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6QYW _struct_ref.pdbx_db_accession 6QYW _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 6QYW _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 6QYW _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _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 8 # 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 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 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 # 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 COSY' 1 isotropic 2 1 1 '2D 1H-1H NOESY' 1 isotropic 3 1 1 '2D 1H-13C HSQC' 1 isotropic 4 1 1 '2D 1H-13C HMBC' 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 5.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength 'TFA salt' _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units 'Not defined' _pdbx_nmr_exptl_sample_conditions.label DMSO_rt _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 '0.7 mg/mL nisin ring A, DMSO' _pdbx_nmr_sample_details.solvent_system DMSO _pdbx_nmr_sample_details.label sample_1 _pdbx_nmr_sample_details.type 'lyophilized powder' _pdbx_nmr_sample_details.details ? # _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 600 _pdbx_nmr_spectrometer.details ? # _pdbx_nmr_refine.entry_id 6QYW _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 2 # _pdbx_nmr_ensemble.entry_id 6QYW _pdbx_nmr_ensemble.conformers_calculated_total_number 150 _pdbx_nmr_ensemble.conformers_submitted_total_number 15 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' # _pdbx_nmr_representative.entry_id 6QYW _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 'structure calculation' Xplor-NIH 2.45 'Schwieters, Kuszewski, Tjandra and Clore' 2 refinement Xplor-NIH 2.45 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' 'CcpNmr Analysis' ? CCPN 4 'peak picking' 'CcpNmr Analysis' ? CCPN # _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 6QYW _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6QYW _struct.title 'Solution NMR of synthetic analogues of nisin and mutacin ring A and ring B - nisin ring A' _struct.pdbx_descriptor DAL-PRO-GLY-CYS-LYS _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 6QYW _struct_keywords.text 'PEPTIDE ANTIBIOTIC, LANTIBIOTIC, ANTIMICROBIAL, BACTERIOCIN, THIOESTER, ANTIBIOTIC' _struct_keywords.pdbx_keywords ANTIBIOTIC # _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_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 covale1 covale both ? A ILE 1 C ? ? ? 1_555 A DBU 2 N ? ? A ILE 1 A DBU 2 1_555 ? ? ? ? ? ? ? 1.345 ? covale2 covale both ? A DBU 2 C ? ? ? 1_555 A DAL 3 N ? ? A DBU 2 A DAL 3 1_555 ? ? ? ? ? ? ? 1.344 ? covale3 covale none ? A DAL 3 CB ? ? ? 1_555 A CYS 7 SG ? ? A DAL 3 A CYS 7 1_555 ? ? ? ? ? ? ? 1.810 ? covale4 covale both ? A DAL 3 C ? ? ? 1_555 A ILE 4 N ? ? A DAL 3 A ILE 4 1_555 ? ? ? ? ? ? ? 1.328 ? covale5 covale both ? A ILE 4 C ? ? ? 1_555 A DHA 5 N ? ? A ILE 4 A DHA 5 1_555 ? ? ? ? ? ? ? 1.345 ? covale6 covale both ? A DHA 5 C ? ? ? 1_555 A LEU 6 N ? ? A DHA 5 A LEU 6 1_555 ? ? ? ? ? ? ? 1.344 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 6QYW _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O 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 ILE 1 1 1 ILE ILE A . n A 1 2 DBU 2 2 2 DBU DBU A . n A 1 3 DAL 3 3 3 DAL DAL A . n A 1 4 ILE 4 4 4 ILE ILE A . n A 1 5 DHA 5 5 5 DHA DHA A . n A 1 6 LEU 6 6 6 LEU LEU A . n A 1 7 CYS 7 7 7 CYS CYS A . n A 1 8 ALA 8 8 8 ALA ALA 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)' 920 ? # _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 2019-09-11 2 'Structure model' 1 1 2019-10-02 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' 'Data collection' 2 2 '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' citation 2 2 'Structure model' citation_author # 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.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component 'nisin ring A' _pdbx_nmr_exptl_sample.concentration 0.7 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units mg/mL _pdbx_nmr_exptl_sample.isotopic_labeling 'natural abundance' # 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 7 ? ? -145.39 -15.76 2 2 DAL A 3 ? ? -35.40 -33.76 3 2 ILE A 4 ? ? -75.36 -86.23 4 2 LEU A 6 ? ? -52.16 -174.18 5 2 CYS A 7 ? ? 88.97 -78.66 6 3 DAL A 3 ? ? -62.68 15.37 7 3 CYS A 7 ? ? -125.15 -61.43 8 4 DAL A 3 ? ? -147.48 -18.95 9 4 CYS A 7 ? ? 85.40 -8.89 10 5 DAL A 3 ? ? -149.81 2.38 11 6 DAL A 3 ? ? -148.94 -9.30 12 6 CYS A 7 ? ? -151.88 -13.28 13 7 DAL A 3 ? ? -36.96 -23.53 14 7 CYS A 7 ? ? -165.22 -20.79 15 8 DAL A 3 ? ? -70.79 68.05 16 8 ILE A 4 ? ? -52.43 76.29 17 8 CYS A 7 ? ? -147.83 -36.49 18 9 DAL A 3 ? ? -51.49 -4.38 19 9 CYS A 7 ? ? -179.20 -4.71 20 10 DAL A 3 ? ? -47.29 -16.08 21 10 LEU A 6 ? ? -169.73 109.49 22 10 CYS A 7 ? ? -151.95 -46.57 23 11 DAL A 3 ? ? -64.28 6.78 24 11 CYS A 7 ? ? -135.85 -48.72 25 12 DAL A 3 ? ? -35.44 -32.81 26 12 CYS A 7 ? ? 176.64 14.88 27 13 DAL A 3 ? ? -38.94 -22.82 28 13 CYS A 7 ? ? 153.67 -53.40 29 14 DAL A 3 ? ? -148.32 25.77 30 15 DAL A 3 ? ? -148.67 -36.86 31 15 CYS A 7 ? ? -159.43 -43.48 # _pdbx_audit_support.funding_organization 'Engineering and Physical Sciences Research Council' _pdbx_audit_support.country 'United Kingdom' _pdbx_audit_support.grant_number EP/L504889/1 _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 ? #