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- PDB-5khb: Structure of Phenol-soluble modulin Alpha1 -

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Basic information

Entry
Database: PDB / ID: 5khb
TitleStructure of Phenol-soluble modulin Alpha1
ComponentsPSM Alpha1
KeywordsSIGNALING PROTEIN / STRUCTURE FROM CYANA 2.1
Function / homologyPhenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 1 peptide
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTowle, K.M. / Lohans, C.T. / Acedo, J.Z. / Miskolzie, M. / van Belkum, M.J. / Vederas, J.C.
CitationJournal: Biochemistry / Year: 2016
Title: Solution Structures of Phenol-Soluble Modulins alpha 1, alpha 3, and beta 2, Virulence Factors from Staphylococcus aureus.
Authors: Towle, K.M. / Lohans, C.T. / Miskolzie, M. / Acedo, J.Z. / van Belkum, M.J. / Vederas, J.C.
History
DepositionJun 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Other / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / pdbx_database_status
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSM Alpha1


Theoretical massNumber of molelcules
Total (without water)2,2911
Polymers2,2911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average
Detailsauthors state the biological assembly is unknown

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Components

#1: Protein/peptide PSM Alpha1


Mass: 2290.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria) / References: UniProt: P0C7Y1*PLUS

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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: solution / Contents: 0.77 mM PSM Alpha1, trifluoroethanol/water / Label: PSM Alpha1 / Solvent system: trifluoroethanol/water
SampleConc.: 0.77 mM / Component: PSM Alpha1 / Isotopic labeling: none
Sample conditionsIonic strength: none Not defined / Label: 25 degrees celsius / pH: 7 / Pressure: 753 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Varian / Manufacturer: Varian / Model: Varian / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
VNMR4.2AVariancollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: 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: 20

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