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- PDB-5kgz: Phenol-soluble modulin Beta2 -

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Basic information

Entry
Database: PDB / ID: 5kgz
TitlePhenol-soluble modulin Beta2
ComponentsModulin Beta2
KeywordsVirulence Factor
Function / homologyPhenol-soluble modulin beta protein / Phenol-soluble modulin beta protein / Antibacterial protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR
AuthorsTowle, K.M. / Lohans, C.T. / Acedo, J.Z. / Van Belkum, M.J. / Miskolzie, M. / Vederas, J.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Alberta Innovates Health Solutions Canada
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 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Structure summary
Category: citation / entity / pdbx_audit_support
Item: _citation.journal_id_CSD / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 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 1.5May 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

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Assembly

Deposited unit
A: Modulin Beta2


Theoretical massNumber of molelcules
Total (without water)4,4591
Polymers4,4591
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 / -
RepresentativeModel #1medoid
Detailsauthor states the biological assembly is unknown

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Components

#1: Protein/peptide Modulin Beta2 / Antibacterial protein 3 / Antibacterial protein 3 homolog / Psm beta2 / Uncharacterized protein


Mass: 4459.106 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: psm beta2, AS858_01105, BN1321_240017, ERS093009_00604, ERS179246_02032, HMPREF3211_00853
Production host: Escherichia coli (E. coli) / References: UniProt: H9BRQ4

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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: 1.9 mM PSMBeta2, trifluoroethanol/water / Label: PSMBeta2 / Solvent system: trifluoroethanol/water
SampleConc.: 1.9 mM / Component: PSMBeta2 / Isotopic labeling: none
Sample conditionsIonic strength: no salt Not defined / Label: 40 degrees celsius / pH: 7 / Pressure: 753 mmHg / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Varian Varian / Manufacturer: Varian / Model: Varian / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.2AVariancollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
NMR representativeSelection criteria: medoid
NMR ensembleConformers submitted total number: 20

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