Crystal structure of ClcF in crystal form 2

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal Structure and Catalytic Mechanism of Chloromuconolactone Dehalogenase Clcf from Rhodococcus Opacus 1Cp.

Roth, C.Janosch, A.D.Kaschabek, S.R.Schloemann, M.Straeter, N.

(2013) Mol Microbiol 88: 254

  • DOI: https://doi.org/10.1111/mmi.12182
  • Primary Citation of Related Structures:  
    3ZNJ, 3ZNU, 3ZO7

  • PubMed Abstract: 

    The actinobacterium Rhodococcus opacus 1CP possesses a so far unique variant of the modified 3-oxoadipate pathway for 3-chlorocatechol degradation. One important feature is the novel dehalogenase ClcF, which converts (4R,5S)-5-chloromuconolactone to E-dienelactone. ClcF is related to muconolactone isomerase (MLI, EC The enzyme has a ferredoxin-type fold and forms a homodecamer of 52-symmetry, typical for the MLI family. The active site is formed by residues from two monomers. The complex structure of an E27A variant with bound substrate in conjunction with mutational studies indicate that E27 acts as the proton acceptor in a univalent single-base syn-dehydrohalogenation mechanism. Despite the evolutionary specialization of ClcF, the conserved active-site structures suggest that the proposed mechanism is representative for the MLI family. Furthermore, ClcF represents a novel type of dehalogenase based on an isomerase scaffold.

  • Organizational Affiliation

    Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
94Rhodococcus opacusMutation(s): 0 
Find proteins for Q8G9L0 (Rhodococcus opacus)
Explore Q8G9L0 
Go to UniProtKB:  Q8G9L0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8G9L0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth E]
EA [auth E]
GA [auth F]
HA [auth F]
BA [auth D],
DA [auth E],
EA [auth E],
GA [auth F],
HA [auth F],
JA [auth G],
KA [auth G],
L [auth A],
M [auth A],
OA [auth H],
P [auth B],
PA [auth H],
Q [auth B],
RA [auth I],
SA [auth I],
T [auth C],
U [auth C],
UA [auth J],
VA [auth J],
Y [auth D],
Z [auth D]
C2 H6 O2
Query on CL

Download Ideal Coordinates CCD File 
CA [auth E]
FA [auth F]
IA [auth G]
K [auth A]
LA [auth H]
CA [auth E],
FA [auth F],
IA [auth G],
K [auth A],
LA [auth H],
MA [auth H],
N [auth B],
O [auth B],
QA [auth I],
R [auth C],
S [auth C],
TA [auth J],
V [auth D],
W [auth D]
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D],
NA [auth H],
X [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.242α = 90
b = 103.574β = 90
c = 141.667γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2013-03-20
    Changes: Atomic model, Other
  • Version 1.3: 2013-04-24
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description