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- PDB-6ry9: Winter flounder 1a-1 in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 6ry9
TitleWinter flounder 1a-1 in SDS micelles
ComponentsPleurocidin-like prepropolypeptide
KeywordsANTIMICROBIAL PROTEIN / Winter Flounder / Antimicrobial peptide / AMP
Function / homologyPleurocidin / Pleurocidin family / defense response to bacterium / extracellular region / Pleurocidin-like prepropolypeptide
Function and homology information
Biological speciesPseudopleuronectes americanus (winter flounder)
MethodSOLUTION NMR / simulated annealing
AuthorsClarke, M. / Mason, A.J.
CitationJournal: To Be Published
Title: Winter flounder 1a-1 in SDS micelles
Authors: Clarke, M. / Mason, A.J.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleurocidin-like prepropolypeptide


Theoretical massNumber of molelcules
Total (without water)2,9661
Polymers2,9661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2860 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 prepropolypeptide


Mass: 2965.640 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Pseudopleuronectes americanus (winter flounder)
References: UniProt: Q90WJ0

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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 WF 1a-1, 50 mM U-98% 2H deuterated sodium dodecyl sulphate (d-25) SDS, 0.05 w/w NA TSP, 90% H2O/10% D2O
Label: WF1a-1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMWF 1a-1NA1
50 mMSDSU-98% 2H deuterated sodium dodecyl sulphate (d-25)1
0.05 w/wTSPNA1
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
10.5 mM peptide in 50 mM deuterated SDS. Solvent: 90% H2O/10% D2O0.5 WF1a-1 mMWF1a-1 TOCSY71 atm298 K
20.5 mM peptide in 50 mM deuterated SDS. Solvent: 90% H2O/10% D2O0.5 WF1a-1 mMWF1a-1 NOESY71 atm298 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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