4WDQ | pdb_00004wdq

Crystal structure of haloalkane dehalogenase LinB32 mutant (L177W) from Sphingobium japonicum UT26

• PDB DOI: https://doi.org/10.2210/pdb4WDQ/pdb

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


• Deposited: 2014-09-09 Released: 2015-12-23 
• Deposition Author(s): Degtjarik, O., Rezacova, P., Chaloupkova, R., Damborsky, J., Kuta-Smatanova, I.
• Funding Organization(s): Czech Academy of Sciences, Czech Science Foundation, Ministry of Education of Czech Republic

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of haloalkane dehalogenase LinB mutant (L177W) from Sphingobium japonicum UT26

Degtjarik, O., Rezacova, P., Chaloupkova, R., Damborsky, J., Kuta-Smatanova, I.

(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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.51 kDa 
• Atom Count: 3,126 
• Modeled Residue Count: 297 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase	A	297	Sphingobium indicum UT26S	Mutation(s): 1  Gene Names: linB 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	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.729	α = 90
b = 68.49	β = 90
c = 81.055	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-23 
Deposition Author(s): Degtjarik, O., Rezacova, P., Chaloupkova, R., Damborsky, J., Kuta-Smatanova, I.

---

Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	RVO 61388963
Czech Academy of Sciences	Czech Republic	RVO 68378050
Czech Science Foundation	Czech Republic	P207/12/0775
Ministry of Education of Czech Republic	Czech Republic	LO1214

Revision History  

• Version 1.0: 2015-12-23
  Type: Initial release
  
• Version 1.1: 2016-10-05
  Changes: Database references
• Version 2.0: 2017-09-06
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations, Refinement description
• Version 2.1: 2019-07-17
  Changes: Data collection
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description