1B6G

HALOALKANE DEHALOGENASE AT PH 5.0 CONTAINING CHLORIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Observed: 0.106 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 refined at 1.15 A resolution.

Ridder, I.S.Rozeboom, H.J.Dijkstra, B.W.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1273-1290

  • DOI: 10.1107/s090744499900534x
  • Primary Citation of Related Structures:  
    1B6G

  • PubMed Abstract: 
  • Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 A resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic least-squares refinement with SHELXL gave a final conv ...

    Crystals of the 35 kDa protein haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 diffract to 1.15 A resolution at cryogenic temperature using synchrotron radiation. Blocked anisotropic least-squares refinement with SHELXL gave a final conventional R factor of 10.51% for all reflections in the 15-1.15 A resolution range. The estimated r.m.s. errors of the model are 0.026 and 0.038 A for protein atoms and all atoms, respectively. The structure comprises all 310 amino acids, with 28 side chains and two peptide bonds in multiple conformations, two covalently linked Pb atoms, 601 water molecules, seven glycerol molecules, one sulfate ion and two chloride ions. Water molecules accounting for alternative solvent structure are modelled with a fixed occupancy of 0.5. The structure is described in detail and compared with previously reported dehalogenase structures refined at 1.9-2.3 A resolution. An analysis of the protein's geometry and stereochemistry reveals eight mean values of bond lengths and angles which deviate significantly from the Engh & Huber parameters, a wide spread in the main-chain omega torsion angle around its ideal value of 180 (6) degrees and a role for C-HcO interactions in satisfying the hydrogen-bond acceptor capacity of main-chain carbonyl O atoms in the central beta-sheet.


    Related Citations: 
    • Kinetic Analysis and X-Ray Structure of Haloalkane Dehalogenase with a Modified Halide-Binding Site
      Krooshof, G.H., Ridder, I.S., Tepper, A.W., Vos, G.J., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W., Janssen, D.B.
      (1998) Biochemistry 37: 15013
    • Crystallographic Analysis of the Catalytic Mechanism of Haloalkane Dehalogenase
      Verschueren, K.H., Seljee, F., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
      (1993) Nature 363: 693
    • Refined X-Ray Structures of Haloalkane Dehalogenase at Ph 6.2 And Ph 8.2 And Implications for the Reaction Mechanism
      Verschueren, K.H., Franken, S.M., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
      (1993) J Mol Biol 232: 856
    • Crystal Structure of Haloalkane Dehalogenase: An Enzyme to Detoxify Halogenated Alkanes
      Franken, S.M., Rozeboom, H.J., Kalk, K.H., Dijkstra, B.W.
      (1991) EMBO J 10: 1297
    • Crystallization of Haloalkane Dehalogenase from Xanthobacter Autotrophicus Gj10
      Rozeboom, H.J., Kingma, J., Janssen, D.B., Dijkstra, B.W.
      (1988) J Mol Biol 200: 611

    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HALOALKANE DEHALOGENASEA310Xanthobacter autotrophicusMutation(s): 2 
Gene Names: dhlA
EC: 3.8.1.5
Find proteins for P22643 (Xanthobacter autotrophicus)
Explore P22643 
Go to UniProtKB:  P22643
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSB
Query on CSB
AL-PEPTIDE LINKINGC3 H6 N O2 Pb SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.145 
  • R-Value Observed: 0.106 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.18α = 90
b = 72.029β = 90
c = 40.909γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-13
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance