5ODZ

CRYSTAL STRUCTURE OF THE BETA-LACTAMASE OXA-163

• PDB DOI: https://doi.org/10.2210/pdb5ODZ/pdb

• Classification: ANTIBIOTIC
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-07 Released: 2017-10-18 
• Deposition Author(s): Lund, B.A., Carlsen, T.J.O., Leiros, H.K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.187 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 

Literature

Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis.

Lund, B.A., Thomassen, A.M., Carlsen, T.J.O., Leiros, H.K.S.

(2017) Acta Crystallogr F Struct Biol Commun 73: 579-587

• PubMed: 28994407 
• DOI: https://doi.org/10.1107/S2053230X17013838
• Primary Citation of Related Structures:  
  5ODZ, 5OE0, 5OE2


• PubMed Abstract: 
  

  The first crystal structures of the class D β-lactamases OXA-181 and OXA-245 were determined to 2.05 and 2.20 Å resolution, respectively; in addition, the structure of a new crystal form of OXA-163 was resolved to 2.07 Å resolution. All of these enzymes are OXA-48-like and have been isolated from different clinical Klebsiella pneumoniae strains and also from other human pathogens such as Pseudomonas aeruginosa and Escherichia coli. Here, enzyme kinetics and thermostability studies are presented, and the new crystal structures are used to explain the observed variations. OXA-245 had the highest melting point (T _m = 55.8°C), as determined by differential scanning calorimetry, compared with OXA-163 (T _m = 49.4°C) and OXA-181 (T _m = 52.6°C). The differences could be explained by the loss of two salt bridges in OXA-163, and an overall decrease in the polarity of the surface of OXA-181 compared with OXA-245.

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Organizational Affiliation: 

Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.

Biological Assembly 1  

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

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 59.24 kDa 
• Atom Count: 4,311 
• Modelled Residue Count: 477 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A [auth B], B [auth D]	252	Enterobacter cloacae	Mutation(s): 0  Gene Names: blaOXA-163 EC: 3.5.2.6
UniProt
Find proteins for F6KZJ2 (Enterobacter cloacae) Explore F6KZJ2  Go to UniProtKB:  F6KZJ2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
CL	C [auth B], D [auth B], H [auth D], I [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth B], F [auth B], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.187 
• R-Value Work: 0.145 
• R-Value Observed: 0.147 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.92	α = 90
b = 121.92	β = 90
c = 160.426	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-18 
Deposition Author(s): Lund, B.A., Carlsen, T.J.O., Leiros, H.K.S.

Revision History  

• Version 1.0: 2017-10-18
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description