Hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis UT26 AT 1.6 A resolution

Experimental Data Snapshot

  • Resolution: 1.58 Å
  • R-Value Free: 0.211 
  • R-Value Observed: 0.149 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 1IZ7


Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.

Marek, J.Vevodova, J.Smatanova, I.K.Nagata, Y.Svensson, L.A.Newman, J.Takagi, M.Damborsky, J.

(2000) Biochemistry 39: 14082-14086

  • DOI: https://doi.org/10.1021/bi001539c
  • Primary Citation of Related Structures:  
    1CV2, 1D07

  • PubMed Abstract: 

    The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.

  • Organizational Affiliation

    Laboratory of Biomolecular Structure and Dynamics, and Department of Inorganic Chemistry, Faculty of Science, Masaryk University, Kotlárská 2, CZ 611 37 Brno, Czech Republic. marek@chemi.muni.cz

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HALOALKANE DEHALOGENASE296Sphingomonas paucimobilisMutation(s): 0 
Find proteins for D4Z2G1 (Sphingobium indicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S))
Explore D4Z2G1 
Go to UniProtKB:  D4Z2G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4Z2G1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.58 Å
  • R-Value Free: 0.211 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.264α = 90
b = 71.669β = 90
c = 72.698γ = 90
Software Package:
Software NamePurpose
MAR345data collection
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-09-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-08-09
    Changes: Data collection, Database references, Refinement description