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- PDB-5kgy: Phenol-soluble modulin Alpha 3 -

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Basic information

Entry
Database: PDB / ID: 5kgy
TitlePhenol-soluble modulin Alpha 3
ComponentsPhenol-soluble modulin alpha 3 peptide
KeywordsSTRUCTURE FROM CYANA 2.1
Function / homology: / Phenol-soluble modulin alpha peptide / Phenol-soluble modulin alpha peptide family / killing of cells of another organism / Phenol-soluble modulin alpha 1 peptide / Phenol-soluble modulin alpha 3 peptide
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTowle, K.M. / Lohans, C.T. / Acedo, J.Z. / Van Belkum, M.J. / Miskolzie, M. / Vederas, J.C.
Funding support Canada, 2items
OrganizationGrant numberCountry
Alberta Innovates Health Solutions Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) 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 / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
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 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenol-soluble modulin alpha 3 peptide


Theoretical massNumber of molelcules
Total (without water)2,6391
Polymers2,6391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2690 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Phenol-soluble modulin alpha 3 peptide


Mass: 2639.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: peptide contains N-terminal formyl methionine
Source: (synth.) Staphylococcus aureus (strain bovine RF122 / ET3-1) (bacteria)
References: UniProt: P0C807, UniProt: P0C7Y1*PLUS
Has protein modificationY

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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: 0.75 mM PSMalpha3, trifluoroethanol/water / Label: PSMalpha3 / Solvent system: trifluoroethanol/water
SampleConc.: 0.75 mM / Component: PSMalpha3 / Isotopic labeling: none
Sample conditionsIonic strength: no salt Not defined / Label: 37 degrees celsius / pH: 7 / Pressure: 753 mmHg / Temperature: 37 C

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.2AVariancollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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