Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 144.27 kDa 
• Atom Count: 10150 
• Modelled Residue Count: 1262 
• Deposited Residue Count: 1292 
• Unique protein chains: 1

3VSK

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

• PDB DOI: 10.2210/pdb3VSK/pdb

• Classification: PENICILLIN-BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus MW2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-25 Released: 2012-10-31 
• Deposition Author(s): Yoshida, H., Tame, J.R., Park, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.300 
• R-Value Work: 0.261 
• R-Value Observed: 0.263 

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

• PubMed: 22846910 
• DOI: 10.1016/j.jmb.2012.07.012
• Primary Citation of Related Structures:  
  3VSK, 3VSL


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 3	A, B	646	Staphylococcus aureus subsp. aureus MW2	Mutation(s): 0  Gene Names: pbp3, MW1504
UniProt
Find proteins for A0A0H3K0B9 (Staphylococcus aureus (strain MW2)) Explore A0A0H3K0B9  Go to UniProtKB:  A0A0H3K0B9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.300 
• R-Value Work: 0.261 
• R-Value Observed: 0.263 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.419	α = 90
b = 143.419	β = 90
c = 189.359	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-25 
• Released Date: 2012-10-31 
Deposition Author(s): Yoshida, H., Tame, J.R., Park, S.Y.

Revision History  

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