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- PDB-1ytr: NMR structure of plantaricin a in dpc micelles, 20 structures -

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Basic information

Entry
Database: PDB / ID: 1ytr
TitleNMR structure of plantaricin a in dpc micelles, 20 structures
ComponentsBacteriocin plantaricin A
KeywordsANTIBIOTIC / pheromone / amphipathic helix / micelle
Function / homologyBacteriocin-type signal sequence / killing of cells of another organism / defense response to bacterium / Bacteriocin plantaricin-A
Function and homology information
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKristiansen, P.E. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure and mode of action of the membrane-permeabilizing antimicrobial peptide pheromone plantaricin A
Authors: Kristiansen, P.E. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin plantaricin A


Theoretical massNumber of molelcules
Total (without water)2,9921
Polymers2,9921
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)20 / 100lowest energy
RepresentativeModel #20lowest energy

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Components

#1: Protein/peptide Bacteriocin plantaricin A


Mass: 2991.594 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Lactobacillus plantarum.
References: UniProt: P80214

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQCOSY
1411H-15N HSQC

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Sample preparation

DetailsContents: 2.9mM PlnA in 100mM DPC, 10% D2O, 90% H20 / Solvent system: 10% D2O, 90% H20
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.1Guntert Prefinement
CYANAstructure solution
TALOS SIMULATED ANNEALINGANNEALINGstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 100 / Conformers submitted total number: 20

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