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- PDB-2kam: NMR structure of delta-toxin from Staphylococcus aureus in CD3OH -

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Basic information

Entry
Database: PDB / ID: 2kam
TitleNMR structure of delta-toxin from Staphylococcus aureus in CD3OH
ComponentsDelta-hemolysin
KeywordsTOXIN / Cytolytic / Cytolysis / Formylation / Hemolysis / Membrane / Secreted / Transmembrane
Function / homologyDelta-hemolysin / Delta lysin family / hemolysis by symbiont of host erythrocytes / toxin activity / host cell plasma membrane / extracellular region / membrane / Delta-hemolysin
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLoureiro-Ferreira, N. / Rodrigues, J. / Brito, R.M.M.
CitationJournal: To be Published
Title: NMR solution structure of delta-toxin in membrane-mimetic environments
Authors: Loureiro-Ferreira, N. / Rodrigues, J. / Birkbeck, T.H. / Brito, R.M.M.
History
DepositionNov 11, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Delta-hemolysin


Theoretical massNumber of molelcules
Total (without water)3,0111
Polymers3,0111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Delta-hemolysin / Delta-lysin / Delta-toxin


Mass: 3010.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: NCTC 10345 / References: UniProt: P0C1V1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
NMR detailsText: The structure of delta-toxin determined in CD3OH. A combination of NOE distance restraints and coupling constants were used.

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Sample preparation

DetailsContents: 3 mM delta-toxin, methanol / Solvent system: methanol
SampleConc.: 3 mM / Component: delta-toxin
Sample conditionspH: 3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felix95Accelrys Software Inc.chemical shift assignment
Felix95Accelrys Software Inc.peak picking
Felix95Accelrys Software Inc.data analysis
Felix95Accelrys Software Inc.processing
VNMR6.1BVariancollection
VNMR6.1BVarianprocessing
X-PLOR NIH2.16.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.16.0refinement
ProcheckNMR3.5.4Laskowski and MacArthurdata analysis
Insight II95Accelrys Software Inc.fme residue modelling
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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