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- PDB-6rsf: NMR structure of pleurocidin KR in SDS micelles -

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Basic information

Entry
Database: PDB / ID: 6rsf
TitleNMR structure of pleurocidin KR in SDS micelles
ComponentsPleurocidin
KeywordsANTIMICROBIAL PROTEIN / AMP / pleurocidin analogue / winter flounder / SDS micelles / sequence optimization
Function / homologyPleurocidin / Pleurocidin family / defense response to bacterium / extracellular region / 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)2,8301
Polymers2,8301
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: 2830.240 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence is a modification of the original isolated peptide pleurocidin
Source: (synth.) Pseudopleuronectes americanus (winter flounder)
References: UniProt: Q90ZY0

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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 KR, 50 mM U-98% 2D deuterated sodium dodecyl sulphate, 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-d, 90% H2O/10% D2O
Details: Peptide powder was dissolve in SDS-d25 micelles at a L/P ratio of 100 (0.5mM peptide and 50mM SDS-d25).
Label: PleurocidinKR in SDS / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMPleurocidin KRNA1
50 mMdeuterated sodium dodecyl sulphateU-98% 2D1
5 mMTris(hydroxymethyl-d3)-amino-d2-methaneU-98% 2D1
0.05 % w/w3-(Trimethylsilyl)propionic-2,2,3,3-dU-99.9% 2D1
Sample conditionsIonic strength: NA Not defined / Label: PKR_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
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
DYNAMODelaglio and Kuszewskistructure calculation
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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