3UMG

Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase Rha0230

• PDB DOI: https://doi.org/10.2210/pdb3UMG/pdb

• Classification: HYDROLASE
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-13 Released: 2012-11-14 
• Deposition Author(s): Chan, P.W.Y., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.272 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Literature

Structural adaptations of L-2-haloacid dehalogenases that enable hydrolytic defluorination

Chan, P.W.Y., To, T.K.W., Petit, P., Tran, C., Waelti, M., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 220.7 kDa 
• Atom Count: 15,601 
• Modelled Residue Count: 1,971 
• Deposited Residue Count: 2,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase	A, B, C, D, E, F, G, H	254	Rhodococcus jostii RHA1	Mutation(s): 0  Gene Names: RHA1_ro00230 EC: 3.8.1.2
UniProt
Find proteins for Q0SK70 (Rhodococcus jostii (strain RHA1)) Explore Q0SK70  Go to UniProtKB:  Q0SK70

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	I [auth A], J [auth C], K [auth D], L [auth E], M [auth F], N [auth G], O [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.272 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.18	α = 90
b = 148.65	β = 90
c = 152.55	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Chan, P.W.Y., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations