4JF6 | pdb_00004jf6

Structure of OXA-23 at pH 7.0

• PDB DOI: https://doi.org/10.2210/pdb4JF6/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-27 Released: 2013-09-25 
• Deposition Author(s): Smith, C.A., Vakulenko, S.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.285 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Structural Basis for Carbapenemase Activity of the OXA-23 beta-Lactamase from Acinetobacter baumannii.

Smith, C.A., Antunes, N.T., Stewart, N.K., Toth, M., Kumarasiri, M., Chang, M., Mobashery, S., Vakulenko, S.B.

(2013) Chem Biol 20: 1107-1115

• PubMed: 24012371 
• DOI: https://doi.org/10.1016/j.chembiol.2013.07.015
• Primary Citation Related Structures: 
  4JF4, 4JF5, 4JF6


• PubMed Abstract: 
  

  Dissemination of Acinetobacter baumannii strains harboring class D β-lactamases producing resistance to carbapenem antibiotics severely limits our ability to treat deadly Acinetobacter infections. Susceptibility determination in the A. baumannii background and kinetic studies with a homogeneous preparation of OXA-23 β-lactamase, the major carbapenemase present in A. baumannii, document the ability of this enzyme to manifest resistance to last-resort carbapenem antibiotics. We also report three X-ray structures of OXA-23: apo OXA-23 at two different pH values, and wild-type OXA-23 in complex with meropenem, a carbapenem substrate. The structures and dynamics simulations reveal an important role for Leu166, whose motion regulates the access of a hydrolytic water molecule to the acyl-enzyme species in imparting carbapenemase activity.

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Organizational Affiliation: 
• Stanford Synchrotron Radiation Lightsource, Stanford University, Menlo Park, CA 94025, USA. Electronic address: [e-mail].

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: 27.98 kDa 
• Atom Count: 2,106 
• Modeled Residue Count: 239 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	243	Acinetobacter baumannii	Mutation(s): 0  Gene Names: ari-1, bla(OXA-23), bla-OXA-23, blaOXA-23, OXA-23, oxa23 EC: 3.5.2.6
UniProt
Find proteins for Q9L4P2 (Acinetobacter baumannii) Explore Q9L4P2  Go to UniProtKB:  Q9L4P2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	C [auth A], D [auth A], E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.285 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 173.662	α = 90
b = 173.662	β = 90
c = 81.449	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Smith, C.A., Vakulenko, S.B.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary