4WVX | pdb_00004wvx

Crystal structure of a phosphotriesterase-like lactonase Gkap in native form

• PDB DOI: https://doi.org/10.2210/pdb4WVX/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus kaustophilus HTA426
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-07 Released: 2015-11-11 
• Deposition Author(s): An, J., Zhang, Y., Yang, G.Y., Feng, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.192 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Engineering a thermostable lactonase for enhanced phosphotriesterase activity against organophosphate pesticides

An, J., Zhang, Y., Yang, G.Y., Feng, Y.

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: 73.33 kDa 
• Atom Count: 5,430 
• Modeled Residue Count: 646 
• Deposited Residue Count: 652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A, B	326	Geobacillus kaustophilus HTA426	Mutation(s): 0  Gene Names: GK1506 EC: 3.5
UniProt
Find proteins for Q5KZU5 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KZU5  Go to UniProtKB:  Q5KZU5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO	C [auth A], D [auth A], F [auth B], G [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.192 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.398	α = 90
b = 89.38	β = 99.33
c = 89.915	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): An, J., Zhang, Y., Yang, G.Y., Feng, Y.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary