5ODZ | pdb_00005odz

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free:
0.187 (Depositor), 0.191 (DCC)
R-Value Work:
0.145 (Depositor), 0.152 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X17013838
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F6KZJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] SDF format, chain H [auth D] SDF format, chain I [auth D] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] mmCIF format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D]	C [auth B], D [auth B], H [auth D], I [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain H [auth D] Focus chain I [auth D] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain H [auth D] Focus chain I [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain J [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain J [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain J [auth D]	E [auth B], F [auth B], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain J [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain J [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on 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 (Depositor), 0.191 (DCC)
R-Value Work: 0.145 (Depositor), 0.152 (DCC)
R-Value Observed: 0.147 (Depositor)

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

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View more in-depth experimental data

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 (Full details and data files)

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