4I97

The crystal structure of glutathione S-transferase SnigGSTD1A from Scaptomyza nigrita in complex with glutathione

• PDB DOI:  https://doi.org/10.2210/pdb4I97/pdb

• Classification: TRANSFERASE
• Organism(s): Scaptomyza nigrita
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-04 Released: 2013-12-04 
• Deposition Author(s): Hailey, A.L., Montfort, W.R., Weichsel, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.273 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 

Literature

Evolution of herbivory by adaption in an ancient detoxification pathway

Gloss, A.D., Vassao, D.G., Schramm, K., Reichelt, M., Hailey, A.L., Rast, T.J., Weichsel, A., Gershenzon, J., Montfort, W.R., Whiteman, N.K.

To be published.

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)

Macromolecule Content

• Total Structure Weight: 47.98 kDa 
• Atom Count: 3,574 
• Modelled Residue Count: 414 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA CLASS 1 GLUTATHIONE S-TRANSFERASE	A, B	208	Scaptomyza nigrita	Mutation(s): 0  Gene Names: GstD1A, GstD1
UniProt
Find proteins for R4S8C5 (Scaptomyza nigrita) Explore R4S8C5  Go to UniProtKB:  R4S8C5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	C [auth A], D [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.273 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.29	α = 90
b = 63.29	β = 90
c = 221.41	γ = 90

Software Package:

Software Name	Purpose
MrBUMP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Hailey, A.L., Montfort, W.R., Weichsel, A.

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description