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- PDB-6rsg: NMR structure of pleurocidin VA in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 6rsg
TitleNMR structure of pleurocidin VA in SDS micelles
ComponentsPleurocidin
KeywordsANTIMICROBIAL PROTEIN / AMP / pleurocidin analogue / winter flounder / SDS micelles / sequence optimization
Function / homologyPleurocidin / Pleurocidin family / defense response to bacterium / lipid binding / extracellular region / membrane / Pleurocidin
Function and homology information
Biological speciesPseudopleuronectes americanus (winter flounder)
MethodSOLUTION NMR / simulated annealing
AuthorsManzo, G. / Mason, A.J.
CitationJournal: Commun Biol / Year: 2020
Title: A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy.
Authors: Manzo, G. / Hind, C.K. / Ferguson, P.M. / Amison, R.T. / Hodgson-Casson, A.C. / Ciazynska, K.A. / Weller, B.J. / Clarke, M. / Lam, C. / Man, R.C.H. / Shaughnessy, B.G.O. / Clifford, M. / ...Authors: Manzo, G. / Hind, C.K. / Ferguson, P.M. / Amison, R.T. / Hodgson-Casson, A.C. / Ciazynska, K.A. / Weller, B.J. / Clarke, M. / Lam, C. / Man, R.C.H. / Shaughnessy, B.G.O. / Clifford, M. / Bui, T.T. / Drake, A.F. / Atkinson, R.A. / Lam, J.K.W. / Pitchford, S.C. / Page, C.P. / Phoenix, D.A. / Lorenz, C.D. / Sutton, J.M. / Mason, A.J.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 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
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Pleurocidin


Theoretical massNumber of molelcules
Total (without water)2,6621
Polymers2,6621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2880 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Pleurocidin


Mass: 2662.077 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Analogue of the antimicrobial peptide pleurocidin, originally extracted from Winter Flounder fish, obtained through sequence optimisation.
Source: (synth.) Pseudopleuronectes americanus (winter flounder)
References: UniProt: P81941

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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 TOCSY
121isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: micelle
Contents: 0.5 mM NA Pleurocidin VA, 50 mM U-98% 2D deuterated sodium dodecyl sulphate (SDS-d25), 5 mM U-98% 2D Tris(hydroxymethyl-d3)-amino-d2-methane, 0.05 % w/w U-99.9% 2D 3-(trimethylsilyl) ...Contents: 0.5 mM NA Pleurocidin VA, 50 mM U-98% 2D deuterated sodium dodecyl sulphate (SDS-d25), 5 mM U-98% 2D Tris(hydroxymethyl-d3)-amino-d2-methane, 0.05 % w/w U-99.9% 2D 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, sodium salt, 90% H2O/10% D2O
Details: Peptide powder was solubilised in SDS-d25 micelles at a L/P ratio of 100.
Label: PleurocidinVA / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPleurocidin VANA1
50 mMdeuterated sodium dodecyl sulphate (SDS-d25)U-98% 2D1
5 mMTris(hydroxymethyl-d3)-amino-d2-methaneU-98% 2D1
0.05 % w/w3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, sodium saltU-99.9% 2D1
Sample conditionsIonic strength: ND Not defined / Label: VA_conditions / pH: 7 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
DYNAMODelaglio and Kuszewskistructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 50

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