2WKI | pdb_00002wki

Crystal structure of the OXA-10 K70C mutant at pH 7.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.202 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2WKI

This is version 1.4 of the entry. See complete history

Literature

Three Factors that Modulate the Activity of Class D Beta-Lactamases and Interfere with the Post-Translational Carboxylation of Lys70.

Vercheval, L.Bauvois, C.Di Paolo, A.Borel, F.Ferrer, J.L.Sauvage, E.Matagne, A.Frere, J.M.Charlier, P.Galleni, M.Kerff, F.

(2010) Biochem J 432: 495

  • DOI: https://doi.org/10.1042/BJ20101122
  • Primary Citation Related Structures: 
    2WGV, 2WGW, 2WKH, 2WKI

  • PubMed Abstract: 

    The activity of class D β-lactamases is dependent on Lys70 carboxylation in the active site. Structural, kinetic and affinity studies show that this post-translational modification can be affected by the presence of a poor substrate such as moxalactam but also by the V117T substitution. Val117 is a strictly conserved hydrophobic residue located in the active site. In addition, inhibition of class D β-lactamases by chloride ions is due to a competition between the side chain carboxylate of the modified Lys70 and chloride ions. Determination of the individual kinetic constants shows that the deacylation of the acyl-enzyme is the rate-limiting step for the wild-type OXA-10 β-lactamase.


  • Organizational Affiliation
    • Laboratory of Biological Macromolecules, Centre for Protein Engineering, Institut de Chimie B6a, University of Liège, Liège 4000, Belgium.

Macromolecule Content 

  • Total Structure Weight: 56.78 kDa 
  • Atom Count: 4,296 
  • Modeled Residue Count: 491 
  • Deposited Residue Count: 496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
BETA-LACTAMASE OXA-10
A, B
248Pseudomonas aeruginosaMutation(s): 1 
EC: 3.5.2.6
UniProt
Find proteins for P14489 (Pseudomonas aeruginosa)
Explore P14489 
Go to UniProtKB:  P14489
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14489
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
O [auth B],
P [auth B],
Q [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.202 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.168 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.46α = 90
b = 96.3β = 90
c = 125.95γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary