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- PDB-2n8o: NMR Solution Structure of Aureocin A53 -

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Basic information

Entry
Database: PDB / ID: 2n8o
TitleNMR Solution Structure of Aureocin A53
ComponentsBacteriocin aureocin A53
KeywordsANTIMICROBIAL PROTEIN / bacteriocin / leaderless bacteriocin
Function / homologyBacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin / killing of cells of another organism / defense response to bacterium / extracellular region / Bacteriocin aureocin A53
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsAcedo, J.Z. / van Belkum, M.J. / Lohans, C.T. / Towle, K.M. / Miskolzie, M. / Vederas, J.C.
CitationJournal: Biochemistry / Year: 2016
Title: Nuclear Magnetic Resonance Solution Structures of Lacticin Q and Aureocin A53 Reveal a Structural Motif Conserved among Leaderless Bacteriocins with Broad-Spectrum Activity.
Authors: Acedo, J.Z. / van Belkum, M.J. / Lohans, C.T. / Towle, K.M. / Miskolzie, M. / Vederas, J.C.
History
DepositionOct 22, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriocin aureocin A53


Theoretical massNumber of molelcules
Total (without water)5,9941
Polymers5,9941
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bacteriocin aureocin A53


Mass: 5994.228 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: aucA / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GPI4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 1 mM Aureocin A53, 0.0001 w/v DSS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMAureocin A53-11
0.0001 w/vDSS-21
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 300 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / 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

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