3VSK

Crystal structure of penicillin-binding protein 3 (PBP3) from methicilin-resistant Staphylococcus aureus in the apo form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structures of Penicillin-Binding Protein 3 (PBP3) from Methicillin-Resistant Staphylococcus aureus in the Apo and Cefotaxime-Bound Forms.

Yoshida, H.Kawai, F.Obayashi, E.Akashi, S.Roper, D.I.Tame, J.R.Park, S.Y.

(2012) J.Mol.Biol. 423: 351-364

  • DOI: 10.1016/j.jmb.2012.07.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Staphylococcus aureus is a widespread Gram-positive opportunistic pathogen, and a methicillin-resistant form (MRSA) is particularly difficult to treat clinically. We have solved two crystal structures of penicillin-binding protein (PBP) 3 (PBP3) from ...

    Staphylococcus aureus is a widespread Gram-positive opportunistic pathogen, and a methicillin-resistant form (MRSA) is particularly difficult to treat clinically. We have solved two crystal structures of penicillin-binding protein (PBP) 3 (PBP3) from MRSA, the apo form and a complex with the β-lactam antibiotic cefotaxime, and used electrospray mass spectrometry to measure its sensitivity to a variety of penicillin derivatives. PBP3 is a class B PBP, possessing an N-terminal non-penicillin-binding domain, sometimes called a dimerization domain, and a C-terminal transpeptidase domain. The model shows a different orientation of its two domains compared to earlier models of other class B PBPs and a novel, larger N-domain. Consistent with the nomenclature of "dimerization domain", the N-terminal region forms an apparently tight interaction with a neighboring molecule related by a 2-fold symmetry axis in the crystal structure. This dimer form is predicted to be highly stable in solution by the PISA server, but mass spectrometry and analytical ultracentrifugation provide unequivocal evidence that the protein is a monomer in solution.


    Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Tsurumi-ku, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Penicillin-binding protein 3
A, B
646Staphylococcus aureus (strain MW2)Mutation(s): 0 
Gene Names: pbp3
Find proteins for A0A0H3K0B9 (Staphylococcus aureus (strain MW2))
Go to UniProtKB:  A0A0H3K0B9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.301 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.261 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 143.419α = 90.00
b = 143.419β = 90.00
c = 189.359γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHARPphasing
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release