2BFN | pdb_00002bfn

The crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane.

• PDB DOI: https://doi.org/10.2210/pdb2BFN/pdb

• Classification: HYDROLASE
• Organism(s): Sphingomonas paucimobilis
• Mutation(s): No 


• Deposited: 2004-12-09 Released: 2006-06-26 
• Deposition Author(s): Banas, P., Otyepka, M., Jerabek, P., Vevodova, J., Bohac, M., Damborsky, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.171 (Depositor) 
• R-Value Work: 
  0.149 (Depositor), 0.378 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Weak Activity of Haloalkane Dehalogenase Linb with 1,2,3-Trichloropropane Revealed by X-Ray Crystallography and Microcalorimetry

Minincova, M., Prokop, Z., Vevodova, J., Nagata, Y., Damborsky, J.

(2007) Appl Environ Microbiol 73: 2005

• PubMed: 17259360 
• DOI: https://doi.org/10.1128/AEM.02416-06
• Primary Citation Related Structures: 
  2BFN


• PubMed Abstract: 
  

  1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound. Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage of a carbon-halogen bond in a wide range of organic halogenated compounds. Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a long time, been considered inactive with TCP, since the reaction cannot be easily detected by conventional analytical methods. Here we demonstrate detection of the weak activity (k(cat) = 0.005 s(-1)) of LinB with TCP using X-ray crystallography and microcalorimetry. This observation makes LinB a useful starting material for the development of a new biocatalyst toward TCP by protein engineering. Microcalorimetry is proposed to be a universal method for the detection of weak enzymatic activities. Detection of these activities is becoming increasingly important for engineering novel biocatalysts using the scaffolds of proteins with promiscuous activities.

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Organizational Affiliation: 
• Loschmidt Laboratories, Masaryk University, Kamenice 5/A4, 625 00 Brno, Czech Republic.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.43 kDa 
• Atom Count: 2,743 
• Modeled Residue Count: 294 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HALOGENALKANE DEHALOGENASE	A	296	Sphingomonas paucimobilis	Mutation(s): 0  EC: 3.8.1.5
UniProt
Find proteins for D4Z2G1 (Sphingobium indicum (strain DSM 16413 / CCM 7287 / MTCC 6362 / UT26 / NBRC 101211 / UT26S)) Explore D4Z2G1  Go to UniProtKB:  D4Z2G1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D2P	B [auth A]	(2S)-2,3-DICHLOROPROPAN-1-OL C3 H6 Cl2 O ZXCYIJGIGSDJQQ-GSVOUGTGSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.171 (Depositor) 
• R-Value Work:  0.149 (Depositor), 0.378 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.571	α = 90
b = 72.142	β = 90
c = 73.311	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-26 
Deposition Author(s): Banas, P., Otyepka, M., Jerabek, P., Vevodova, J., Bohac, M., Damborsky, J.

Revision History  

• Version 1.0: 2006-06-26
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description