7ODA

OXA-48-like Beta-lactamase OXA-436


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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

Biochemical and biophysical characterization of the OXA-48-like carbapenemase OXA-436.

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

(2021) Acta Crystallogr F Struct Biol Commun 77: 312-318

  • DOI: https://doi.org/10.1107/S2053230X21008645
  • Primary Citation of Related Structures:  
    7ODA

  • PubMed Abstract: 

    The crystal structure of the class D β-lactamase OXA-436 was solved to a resolution of 1.80 Å. Higher catalytic rates were found at higher temperatures for the clinically important antibiotic imipenem, indicating better adaptation of OXA-436 to its mesophilic host than OXA-48, which is believed to originate from an environmental source. Furthermore, based on the most populated conformations during 100 ns molecular-dynamics simulations, it is postulated that the modulation of activity involves conformational shifts of the α3-α4 and β5-β6 loops. While these changes overall do not cause clinically significant shifts in the resistance profile, they show that antibiotic-resistance enzymes exist in a continuum. It is believed that these seemingly neutral differences in the sequence exist on a path leading to significant changes in substrate selectivity.


  • Organizational Affiliation

    The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B, C, D
244Enterobacter asburiaeMutation(s): 0 
Gene Names: blaOXA-436
EC: 3.5.2.6
UniProt
Find proteins for A0A0S2C593 (Enterobacter asburiae)
Explore A0A0S2C593 
Go to UniProtKB:  A0A0S2C593
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S2C593
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
K [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
K [auth C],
L [auth C],
M [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth B],
J [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A, B, C, D
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.116α = 90
b = 94.571β = 109.89
c = 87.762γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description