4QXZ

Crystal structure of a hypothetical protein from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of YwpF from Staphylococcus aureus reveals its architecture comprised of a beta-barrel core domain resembling type VI secretion system proteins and a two-helix pair.

Lee, S.J.Lee, K.Y.Lee, K.Y.Kim, D.G.Kim, S.J.Lee, B.J.

(2015) Proteins 83: 781-788

  • DOI: https://doi.org/10.1002/prot.24774
  • Primary Citation of Related Structures:  
    4QXZ

  • PubMed Abstract: 

    The ywpF gene (SAV2097) of the Staphylococcus aureus strain Mu50 encodes the YwpF protein, which may play a role in antibiotic resistance. Here, we report the first crystal structure of the YwpF superfamily from S. aureus at 2.5-Å resolution. The YwpF structure consists of two regions: an N-terminal core β-barrel domain that shows structural similarity to type VI secretion system (T6SS) proteins (e.g., Hcp1, Hcp3, and EvpC) and a C-terminal two-helix pair. Although the monomer structure of S. aureus YwpF resembles those of T6SS proteins, the dimer/tetramer model of S. aureus YwpF is distinct from the functionally important hexameric ring of T6SS proteins. We therefore suggest that the S. aureus YwpF may have a different function compared to T6SS proteins.


  • Organizational Affiliation

    The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-Gu, Seoul, 151-742, Korea.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
166Staphylococcus aureus subsp. aureus Mu50Mutation(s): 0 
Gene Names: SAV2097
UniProt
Find proteins for A0A0H3JSS7 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore A0A0H3JSS7 
Go to UniProtKB:  A0A0H3JSS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3JSS7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.391α = 90
b = 90.376β = 90
c = 110.637γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AutoSolphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release