3ISO

Crystal structure of 26 kDa GST of Clonorchis sinensis in P3221 symmetry

• PDB DOI: https://doi.org/10.2210/pdb3ISO/pdb

• Classification: TRANSFERASE
• Organism(s): Clonorchis sinensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-27 Released: 2010-09-08 
• Deposition Author(s): Han, Y.H., Seo, H.A., Kim, G.H., Chung, Y.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Literature

A histidine substitution confers metal binding affinity to a Schistosoma japonicum Glutathione S-transferase.

Han, Y.H., Seo, H.A., Kim, G.H., Lee, C.K., Kang, Y.K., Ryu, K.H., Chung, Y.J.

(2010) Protein Expr Purif 73: 74-77

• PubMed: 20347989 
• DOI: https://doi.org/10.1016/j.pep.2010.03.014
• Primary Citation of Related Structures:  
  3ISO


• PubMed Abstract: 
  

  Glutathione S-transferases (GSTs) are multifunctional enzymes that are used as fusion tags on recombinant proteins in mammalian and Escherichia coli expression systems. We recently found that the Schistosoma japonicum GST (SjGST) displays weak Ni(2+) ion binding affinity. Glu26 and His79 were assumed to be its Ni(2+) binding sites based on the structure of the 26-kDa Clonorchis sinensis GST. To enhance SjGST Ni(2+) binding affinity, Glu26 was mutated to His. SjGST-E26H was expressed and purified at a high concentration of imidazole to a higher purity than wild type SjGST. In addition, human biotin protein ligase fused to SjGST-E26H was purified with a immobilized Ni affinity column.

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Organizational Affiliation: 

Department of Biochemistry, Chungbuk National University, Cheongju 361-763, Republic of Korea.

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: 51.65 kDa 
• Atom Count: 3,875 
• Modelled Residue Count: 436 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione transferase	A, B	218	Clonorchis sinensis	Mutation(s): 0
UniProt
Find proteins for Q25595 (Clonorchis sinensis) Explore Q25595  Go to UniProtKB:  Q25595

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	C [auth A], J [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	D [auth A], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.226 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.39	α = 90
b = 96.39	β = 90
c = 115.428	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Han, Y.H., Seo, H.A., Kim, G.H., Chung, Y.J.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description