4C6H

Haloalkane dehalogenase with 1-hexanol

• PDB DOI: https://doi.org/10.2210/pdb4C6H/pdb

• Classification: HYDROLASE
• Organism(s): Paracoccaceae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-18 Released: 2014-05-14 
• Deposition Author(s): Novak, H.R., Sayer, C., Isupov, M., Gotz, D., Spragg, A.M., Littlechild, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.187 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Biochemical and Structural Characterisation of a Haloalkane Dehalogenase from a Marine Rhodobacteraceae.

Novak, H.R., Sayer, C., Isupov, M.N., Gotz, D., Spragg, A.M., Littlechild, J.A.

(2014) FEBS Lett 588: 1616

• PubMed: 24613925 
• DOI: https://doi.org/10.1016/j.febslet.2014.02.056
• Primary Citation of Related Structures:  
  4BRZ, 4C6H


• PubMed Abstract: 
  

  A putative haloalkane dehalogenase has been identified in a marine Rhodobacteraceae and subsequently cloned and over-expressed in Escherichia coli. The enzyme has highest activity towards the substrates 1,6-dichlorohexane, 1-bromooctane, 1,3-dibromopropane and 1-bromohexane. The crystal structures of the enzyme in the native and product bound forms reveal a large hydrophobic active site cavity. A deeper substrate binding pocket defines the enzyme preference towards substrates with longer carbon chains. Arg136 at the bottom of the substrate pocket is positioned to bind the distal halogen group of extended di-halogenated substrates.

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Organizational Affiliation: 

The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.95 kDa 
• Atom Count: 2,755 
• Modelled Residue Count: 291 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HALOALKANE DEHALOGENASE	A	291	Paracoccaceae	Mutation(s): 0  EC: 3.8.1.5
UniProt
Find proteins for A0A067XG66 (Paracoccaceae) Explore A0A067XG66  Go to UniProtKB:  A0A067XG66

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
HE2	D [auth A]	HEXAN-1-OL C6 H14 O ZSIAUFGUXNUGDI-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.187 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.45	α = 90
b = 71.41	β = 90
c = 59.75	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Novak, H.R., Sayer, C., Isupov, M., Gotz, D., Spragg, A.M., Littlechild, J.A.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description