3VPT

Crystal structure of Bombyx mori sigma-class glutathione transferase in apo form

• PDB DOI: https://doi.org/10.2210/pdb3VPT/pdb

• Classification: TRANSFERASE
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-13 Released: 2013-03-06 
• Deposition Author(s): Yamamoto, K., Higashiura, A., Suzuki, M., Nakagawa, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Crystal structure of a Bombyx mori sigma-class glutathione transferase exhibiting prostaglandin E synthase activity

Yamamoto, K., Higashiura, A., Suzuki, M., Aritake, K., Urade, Y., Uodome, N., Nakagawa, A.

(2013) Biochim Biophys Acta 1830: 3711-3718

• PubMed: 23458683 
• DOI: https://doi.org/10.1016/j.bbagen.2013.02.021
• Primary Citation of Related Structures:  
  3VPQ, 3VPT


• PubMed Abstract: 
  

  Glutathione transferases (GSTs) are members of a major family of detoxification enzymes. Here, we report the crystal structure of a sigma-class GST of Bombyx mori, bmGSTS1, to gain insight into the mechanism catalysis.

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Organizational Affiliation: 

Kyushu University Graduate School, Fukuoka, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.44 kDa 
• Atom Count: 1,761 
• Modelled Residue Count: 203 
• Deposited Residue Count: 204 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase sigma	A	204	Bombyx mori	Mutation(s): 0  Gene Names: GST sigma EC: 2.5.1.18
UniProt
Find proteins for Q5CCJ4 (Bombyx mori) Explore Q5CCJ4  Go to UniProtKB:  Q5CCJ4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	K [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	F [auth A], G [auth A], H [auth A], L [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PGO	B [auth A], C [auth A], D [auth A], E [auth A], I [auth A], J [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.253 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.128	α = 90
b = 56.128	β = 90
c = 209.893	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-06 
Deposition Author(s): Yamamoto, K., Higashiura, A., Suzuki, M., Nakagawa, A.

Revision History  

• Version 1.0: 2013-03-06
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations