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- PDB-2ls9: Pleurocidin-NH2 -

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Basic information

Entry
Database: PDB / ID: 2ls9
TitlePleurocidin-NH2
ComponentsPleurocidin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
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, torsion angle dynamics
Model detailsclosest to the average, model 10
AuthorsVermeer, L.S. / Kozlowska, J. / Mason, J.A.
CitationJournal: To be Published
Title: All Atom Simulations of the Initial Binding of Magainin and Pleurocidin to Membranes Comprising of a Mixture of Anionic and Zwitterionic Lipids
Authors: Vermeer, L.S. / Kozlowska, J. / Lorenz, C.D. / Mason, J.A.
History
DepositionApr 24, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleurocidin


Theoretical massNumber of molelcules
Total (without water)2,7181
Polymers2,7181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Pleurocidin


Mass: 2718.183 Da / Num. of mol.: 1 / Source method: obtained synthetically
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-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 5 mM TRIS, 1 mM pleurocidin, 100 mM [U-2H] SDS, 0.05 % TSP, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMTRIS-11
1 mMpleurocidin-21
100 mMSDS-3[U-2H]1
0.05 %TSP-41
Sample conditionsIonic strength: 5 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
AQUARullmann, Doreleijers and Kapteindata analysis
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
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: 10

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