3UMC | pdb_00003umc

Crystal Structure of the L-2-Haloacid Dehalogenase PA0810

• PDB DOI: https://doi.org/10.2210/pdb3UMC/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-13 Released: 2012-11-14 
• Deposition Author(s): Petit, P., 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: 2.15 Å
• R-Value Free: 
  0.236 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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)

Macromolecule Content

• Total Structure Weight: 116.35 kDa 
• Atom Count: 7,892 
• Modelled Residue Count: 930 
• Deposited Residue Count: 1,016 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
haloacid dehalogenase	A, B, C, D	254	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: PA0810 EC: 3.8.1.2
UniProt
Find proteins for Q9I5C9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I5C9  Go to UniProtKB:  Q9I5C9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth B], G [auth C], I [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth C], J [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.236 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.424	α = 90
b = 123.867	β = 90.97
c = 125.599	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Petit, P., 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: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary