7KCW

Crystal structure of S. aureus penicillin-binding protein 4 (PBP4) mutant (R200L) in complex with nafcillin

• PDB DOI: https://doi.org/10.2210/pdb7KCW/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-10-07 Released: 2021-06-30 
• Deposition Author(s): Alexander, J.A., Strynadka, N.C.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.212 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

PBP4-mediated beta-lactam resistance among clinical strains of Staphylococcus aureus.

Satishkumar, N., Alexander, J.A.N., Poon, R., Buggeln, E., Argudin, M.A., Strynadka, N.C.J., Chatterjee, S.S.

(2021) J Antimicrob Chemother 76: 2268-2272

• PubMed: 34151961 
• DOI: https://doi.org/10.1093/jac/dkab201
• Primary Citation of Related Structures:  
  7KCV, 7KCW, 7KCX, 7KCY


• PubMed Abstract: 
  

  PBP4, a low-molecular-weight PBP in Staphylococcus aureus, is not considered to be a classical mediator of β-lactam resistance. Previous studies carried out by our group with laboratory strains of S. aureus demonstrated the ability of PBP4 to produce β-lactam resistance through mutations associated with the pbp4 promoter and/or gene. Recent studies of β-lactam-resistant clinical isolates of S. aureus have reported similar mutations associated with pbp4.

---

Organizational Affiliation: 

Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 41.72 kDa 
• Atom Count: 3,187 
• Modelled Residue Count: 360 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein 4	A	367	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1  Gene Names: pbp4, SACOL0699
UniProt
Find proteins for A0A0H2WY27 (Staphylococcus aureus (strain COL)) Explore A0A0H2WY27  Go to UniProtKB:  A0A0H2WY27

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NFF (Subject of Investigation/LOI)	B [auth A]	(2R,4S)-2-[(1R)-1-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid C21 H24 N2 O5 S XDLYHUOUOKHAMD-DKSSEZFCSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.212 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.15	α = 90
b = 82.87	β = 90
c = 104.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Alexander, J.A., Strynadka, N.C.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2021-08-18
  Changes: Database references
• Version 1.2: 2021-09-29
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description