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

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Basic information

Entry
Database: PDB / ID: 6qtf
TitleSolution NMR of synthetic analogues of nisin and mutacin ring A and ring B - Mutacin I Ring B, major conformer
ComponentsDCY-LEU-GLY-ALA-THR
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 analogue.
Authors: Dickman, R. / Danelius, E. / Mitchell, S.A. / Hansen, D.F. / Erdelyi, M. / Tabor, A.B.
History
DepositionFeb 25, 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 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DCY-LEU-GLY-ALA-THR


Theoretical massNumber of molelcules
Total (without water)4641
Polymers4641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area600 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 DCY-LEU-GLY-ALA-THR


Mass: 463.549 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: 13.0 mg/mL Mutacin I ring B, DMSO
Details: HPLC purified peptide (TFA salt) was dissolved directly in DMSO
Label: sample_1 / Solvent system: DMSO
SampleConc.: 13.0 mg/mL / Component: Mutacin I ring B / 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
NameDeveloperClassification
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
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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