3BYD | pdb_00003byd

Crystal structure of beta-lactamase OXY-1-1 from Klebsiella oxytoca


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.225 (Depositor), 0.288 (DCC) 
  • R-Value Work: 
    0.182 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Structural insights into the broadened substrate profile of the extended-spectrum beta-lactamase OXY-1-1 from Klebsiella oxytoca

Liang, Y.-H.Gao, R.Su, X.-D.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1460-1467

  • DOI: https://doi.org/10.1107/S090744491203466X
  • Primary Citation Related Structures: 
    3BYD

  • PubMed Abstract: 

    Klebsiella oxytoca is a pathogen that causes serious infections in hospital patients. It shows resistance to many clinically used β-lactam antibiotics by producing chromosomally encoded OXY-family β-lactamases. Here, the crystal structure of an OXY-family β-lactamase, OXY-1-1, determined at 1.93 Å resolution is reported. The structure shows that the OXY-1-1 β-lactamase has a typical class A β-lactamase fold and exhibits greater similarity to CTX-M-type β-lactamases than to TEM-family or SHV-family β-lactamases. It is also shown that the enzyme provides more space around the active cavity for the R(1) and R(2) substituents of β-lactam antibiotics. The half-positive/half-negative distribution of surface electrostatic potential in the substrate-binding pocket indicates the preferred properties of substrates or inhibitors of the enzyme. The results reported here provide a structural basis for the broadened substrate profile of the OXY-family β-lactamases.


  • Organizational Affiliation
    • State Key Laboratory of Protein and Plant Gene Research and Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, People's Republic of China. liangyh@pku.edu.cn

Macromolecule Content 

  • Total Structure Weight: 29.05 kDa 
  • Atom Count: 2,178 
  • Modeled Residue Count: 261 
  • Deposited Residue Count: 267 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase OXY-1267Klebsiella oxytocaMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for P22391 (Klebsiella oxytoca)
Explore P22391 
Go to UniProtKB:  P22391
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22391
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.225 (Depositor), 0.288 (DCC) 
  • R-Value Work:  0.182 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.545α = 90
b = 73.431β = 90
c = 84.561γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-11-07
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description