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- PDB-6qyv: Solution NMR of synthetic analogues of nisin and mutacin ring A a... -

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Basic information

Entry
Database: PDB / ID: 6qyv
TitleSolution NMR of synthetic analogues of nisin and mutacin ring A and ring B - Mutacin I Ring A (Ser2, Ala5, Ala8) analogue
ComponentsPHE-SER-DAL-LEU-ALA-LEU-CYS-ALA
KeywordsANTIBIOTIC / PEPTIDE ANTIBIOTIC / LANTIBIOTIC / ANTIMICROBIAL / BACTERIOCIN / THIOESTER
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsDickman, R. / Mitchell, S.A. / Figueiredo, A. / Hansen, D.F. / Tabor, A.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/L504889/1 United Kingdom
Citation
Journal: J.Org.Chem. / Year: 2019
Title: Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B.
Authors: Dickman, R. / Mitchell, S.A. / Figueiredo, A.M. / Hansen, D.F. / Tabor, A.B.
#1: Journal: To Be Published
Title: 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.
Authors: Dickman, R. / Danelius, E. / Mitchell, S.A. / Hansen, D.F. / Erdelyi, M. / Tabor, A.B.
History
DepositionMar 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHE-SER-DAL-LEU-ALA-LEU-CYS-ALA


Theoretical massNumber of molelcules
Total (without water)7951
Polymers7951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area980 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide PHE-SER-DAL-LEU-ALA-LEU-CYS-ALA


Mass: 794.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H COSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-13C HMBC

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Sample preparation

DetailsType: lyophilized powder
Contents: 0.7 mg/mL Mutacin I Ring A (Ser2, Ala5, Ala8) analogue, DMSO
Label: sample_1 / Solvent system: DMSO
SampleConc.: 0.7 mg/mL / Component: Mutacin I Ring A (Ser2, Ala5, Ala8) analogue / Isotopic labeling: natural abundance
Sample conditionsIonic strength: TFA salt Not defined / Label: DMSO_rt / pH: 5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.45Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Xplor-NIH2.45Schwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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