6RJ7 | pdb_00006rj7

Crystal structure of the 19F labelled OXA-48


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.210 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.177 (Depositor) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

19F NMR Monitoring of Reversible Protein Post-Translational Modifications: Class D beta-Lactamase Carbamylation and Inhibition.

van Groesen, E.Lohans, C.T.Brem, J.Aertker, K.M.J.Claridge, T.D.W.Schofield, C.J.

(2019) Chemistry 25: 11837-11841

  • DOI: https://doi.org/10.1002/chem.201902529
  • Primary Citation Related Structures: 
    6RJ7

  • PubMed Abstract: 

    Bacterial production of β-lactamases with carbapenemase activity is a global health threat. The active sites of class D carbapenemases such as OXA-48, which is of major clinical importance, uniquely contain a carbamylated lysine residue which is essential for catalysis. Although there is significant interest in characterizing this post-translational modification, and it is a promising inhibition target, protein carbamylation is challenging to monitor in solution. We report the use of 19 F NMR spectroscopy to monitor the carbamylation state of 19 F-labelled OXA-48. This method was used to investigate the interactions of OXA-48 with clinically used serine β-lactamase inhibitors, including avibactam and vaborbactam. Crystallographic studies on 19 F-labelled OXA-48 provide a structural rationale for the sensitivity of the 19 F label to active site interactions. The overall results demonstrate the use of 19 F NMR to monitor reversible covalent post-translational modifications.


  • Organizational Affiliation
    • Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK.

Macromolecule Content 

  • Total Structure Weight: 57.23 kDa 
  • Atom Count: 4,317 
  • Modeled Residue Count: 487 
  • Deposited Residue Count: 490 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B
245Klebsiella pneumoniaeMutation(s): 1 
Gene Names: bla OXA-48blaOXA-48KPE71T_00045
EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae)
Explore Q6XEC0 
Go to UniProtKB:  Q6XEC0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6XEC0
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
K5H
Query on K5H
A, B
L-PEPTIDE LINKINGC6 H10 F3 N O4 SCYS
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.210 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.177 (Depositor) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.36α = 90
b = 58.03β = 91.49
c = 66.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
SHELXDphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description