4L5O

Crystal structure of 26 kDa GST D26H mutant of Clonorchis sinensis

• PDB DOI:  https://doi.org/10.2210/pdb4L5O/pdb

• Classification: TRANSFERASE
• Organism(s): Clonorchis sinensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-06-11 Released: 2013-09-11 
• Deposition Author(s): Chung, Y.J., Han, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Crystal structures of 26kDa Clonorchis sinensis glutathione S-transferase reveal zinc binding and putative metal binding.

Han, Y.H., Hong, S.J., Cheong, H.K., Chung, Y.J.

(2013) Biochem Biophys Res Commun 438: 457-461

• PubMed: 23916611 
• DOI: https://doi.org/10.1016/j.bbrc.2013.07.102
• Primary Citation of Related Structures:  
  4L5L, 4L5O


• PubMed Abstract: 
  

The crystal structures of CsGST in two different space groups revealed that Asp26 and His79 coordinate a zinc ion. In one space group, His46 of an adjacent molecule participates in the coordination within 2.0Å. In the other space group, Asp26, His79 and a water molecule coordinate a zinc ion. The CsGST-D26H structure showed that four histidine residues - His26 and His79 from one molecule and the same residues from a symmetry-related neighboring molecule - coordinate a zinc ion. The coordinated zinc ions are located between two molecules and mediate molecular contacts within the crystal.

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Organizational Affiliation: 

Division of Magnetic Resonance Research, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Republic of Korea.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 76.9 kDa 
• Atom Count: 5,643 
• Modelled Residue Count: 651 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione transferase	A, B, C	218	Clonorchis sinensis	Mutation(s): 1  Gene Names: CSKR_11935s EC: 2.5.1.18

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.37	α = 90
b = 98.37	β = 90
c = 178.501	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-11 
Deposition Author(s): Chung, Y.J., Han, Y.H.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2015-06-17
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description