6S06

Crystal structure of haloalkane dehalogenase LinB D147C+L177C mutant (LinB73) from Sphingobium japonicum UT26

• PDB DOI: https://doi.org/10.2210/pdb6S06/pdb

• Classification: HYDROLASE
• Organism(s): Sphingobium indicum UT26S
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-06-14 Released: 2020-07-15 
• Deposition Author(s): Iermak, I., Mesters, J.R., Degtjarik, O., Chaloupkova, R., Kuta Smatanova, I.
• Funding Organization(s): Czech Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 

Starting Model: experimental

Literature

Description of Transport Tunnel in Haloalkane Dehalogenase Variant LinB D147C+L177C from Sphingobium japonicum

Iermak, I., Degtjarik, O., Havlickova, P., Kuty, M., Chaloupkova, R., Damborsky, J., Prudnikova, T., Kuta Smatanova, I.

(2021) Catalysts 

• DOI: https://doi.org/10.3390/catal11010005

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: 34.06 kDa 
• Atom Count: 2,531 
• Modelled Residue Count: 294 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	302	Sphingobium indicum UT26S	Mutation(s): 2  Gene Names: linB, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.230 
• R-Value Work: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.724	α = 90
b = 68.709	β = 90
c = 80.614	γ = 90

Software Package:

Software Name	Purpose
SHELXL	refinement
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Iermak, I., Mesters, J.R., Degtjarik, O., Chaloupkova, R., Kuta Smatanova, I.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	GACR (17-24321S)

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2021-01-27
  Changes: Database references, Derived calculations
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description