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- PDB-6rz1: Winter flounder 3 in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 6rz1
TitleWinter flounder 3 in SDS micelles
ComponentsPleurocidin-like peptide WF3
KeywordsANTIMICROBIAL PROTEIN / winter flounder / AMP / antimicrobial peptide / pleurocidin-like
Function / homologyPleurocidin / Pleurocidin family / defense response to bacterium / extracellular region / Pleurocidin-like peptide WF3
Function and homology information
Biological speciesPseudopleuronectes americanus (winter flounder)
MethodSOLUTION NMR / simulated annealing
AuthorsMason, A.J. / Clarke, M.
CitationJournal: To Be Published
Title: Structure of winter flounder AMP 3
Authors: Mason, A.J. / Clarke, M.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleurocidin-like peptide WF3


Theoretical massNumber of molelcules
Total (without water)2,6311
Polymers2,6311
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2620 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)100 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Pleurocidin-like peptide WF3


Mass: 2631.112 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Pseudopleuronectes americanus (winter flounder)
References: UniProt: Q90VW7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TOCSY
121isotropic12D NOESY

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Sample preparation

DetailsType: micelle
Contents: 0.5 mM NA Peptide, 50 mM U-98% Dodecyl-d25 sulfate sodium salt, SDS-d25 SDS, 0.005 % w/w NA TSP, 90% H2O/10% D2O
Details: 0.5 mM WF in 50 mM SDS micelles / Label: WF3 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPeptideNA1
50 mMSDSU-98% Dodecyl-d25 sulfate sodium salt, SDS-d251
0.005 % w/wTSPNA1
Sample conditionsIonic strength: 0.5 mM WF3 mM / Label: WF3 / pH: 7.0 / 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
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
DYNAMODelaglio and Kuszewskistructure calculation
DYNAMODelaglio and Kuszewskirefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 100

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