2XSR

Crystal structure of wild type Acinetobacter radioresistens catechol 1,2 dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

X-Ray Crystallography, Mass Spectrometry and Single Crystal Microspectrophotometry: A Multidisciplinary Characterization of Catechol 1,2 Dioxygenase.

Micalella, C.Martignon, S.Bruno, S.Pioselli, B.Caglio, R.Valetti, F.Pessione, E.Giunta, C.Rizzi, M.

(2011) Biochim Biophys Acta 1814: 817

  • DOI: https://doi.org/10.1016/j.bbapap.2010.09.008
  • Primary Citation of Related Structures:  
    2XSR, 2XSU, 2XSV

  • PubMed Abstract: 

    Intradiol-cleaving catechol 1,2 dioxygenases are Fe(III) dependent enzymes that act on catechol and substituted catechols, including chlorocatechols pollutants, by inserting molecular oxygen in the aromatic ring. Members of this class are the object of intense biochemical investigations aimed at the understanding of their catalytic mechanism, particularly for designing mutants with selected catalytic properties. We report here an in depth investigation of catechol 1,2 dioxygenase IsoB from Acinetobacter radioresistens LMG S13 and its A72G and L69A mutants. By applying a multidisciplinary approach that includes high resolution X-rays crystallography, mass spectrometry and single crystal microspectrophotometry, we characterised the phospholipid bound to the enzyme and provided a structural framework to understand the inversion of substrate specificity showed by the mutants. Our results might be of help for the rational design of enzyme mutants showing a biotechnologically relevant substrate specificity, particularly to be used in bioremediation. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Parma, Viale GP. Usberti 23/A, 43100 Parma, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATECHOL 1,2 DIOXYGENASE312Acinetobacter radioresistensMutation(s): 0 
UniProt
Find proteins for Q9F103 (Acinetobacter radioresistens)
Explore Q9F103 
Go to UniProtKB:  Q9F103
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F103
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PIE
Query on PIE

Download Ideal Coordinates CCD File 
C [auth A]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL
C43 H80 O13 P
PDLAMJKMOKWLAJ-OJERQSHOSA-M
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.645α = 90
b = 79.447β = 132.5
c = 83.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-08
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Data collection, Other, Version format compliance
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description