5LKA

Crystal structure of haloalkane dehalogenase LinB 140A+143L+177W+211L mutant (LinB86) from Sphingobium japonicum UT26 at 1.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5LKA/pdb

• Classification: HYDROLASE
• Organism(s): Sphingobium indicum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-21 Released: 2016-10-05 
• Deposition Author(s): Degtjarik, O., Rezacova, P., Iermak, I., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 

Literature

Engineering a de novo transport tunnel.

Brezovsky, J., Babkova, P., Degtjarik, O., Fortova, A., Gora, A., Iermak, I., Rezacova, P., Dvorak, P., Kuta Smatanova, I., Prokop, Z., Chaloupkova, R., Damborsky, J.

(2016) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.6b02081

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: 33.82 kDa 
• Atom Count: 2,988 
• Modelled Residue Count: 301 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	301	Sphingobium indicum	Mutation(s): 4  Gene Names: linB, dhaA, SJA_C1-19590 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN	B [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.139 
• R-Value Observed: 0.140 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.867	α = 90
b = 68.362	β = 90
c = 80.648	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Degtjarik, O., Rezacova, P., Iermak, I., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description