3UM9

Crystal Structure of the Defluorinating L-2-Haloacid Dehalogenase Bpro0530

• PDB DOI: https://doi.org/10.2210/pdb3UM9/pdb

• Classification: HYDROLASE
• Organism(s): Polaromonas sp. JS666
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-12 Released: 2012-11-14 
• Deposition Author(s): Chan, P.W.Y., Savchenko, A., Yakunin, A.F., Edwards, E.A., Pai, E.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.199 
• R-Value Work: 0.144 
• R-Value Observed: 0.147 

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)

Macromolecule Content

• Total Structure Weight: 51.37 kDa 
• Atom Count: 3,659 
• Modelled Residue Count: 450 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloacid dehalogenase, type II	A, B	230	Polaromonas sp. JS666	Mutation(s): 0  Gene Names: Bpro0530, Bpro_0530 EC: 3.8.1.2
UniProt
Find proteins for Q12G50 (Polaromonas sp. (strain JS666 / ATCC BAA-500)) Explore Q12G50  Go to UniProtKB:  Q12G50

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.199 
• R-Value Work: 0.144 
• R-Value Observed: 0.147 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.64	α = 90
b = 96.64	β = 90
c = 92.03	γ = 120

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