4JED | pdb_00004jed

Crystal structure of glutathione s-transferase mrad2831_1084 (target efi-507060) from methylobacterium radiotolerans jcm 2831, complex with glutathione sulfonate

• PDB DOI: https://doi.org/10.2210/pdb4JED/pdb

• Classification: TRANSFERASE
• Organism(s): Methylobacterium radiotolerans JCM 2831
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-02-26 Released: 2013-03-13 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.131 (Depositor), 0.138 (DCC) 
• R-Value Work: 
  0.114 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glutathione S-transferase (TARGET EFI-507060) from Methylobacterium radiotolerans

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

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: 27.16 kDa 
• Atom Count: 2,244 
• Modeled Residue Count: 212 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTATHIONE S-TRANSFERASE	A	237	Methylobacterium radiotolerans JCM 2831	Mutation(s): 0  Gene Names: Mrad2831_1084
UniProt
Find proteins for B1M0X3 (Methylobacterium radiotolerans (strain ATCC 27329 / DSM 1819 / JCM 2831 / NBRC 15690 / NCIMB 10815 / 0-1)) Explore B1M0X3  Go to UniProtKB:  B1M0X3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTS	C [auth A]	GLUTATHIONE SULFONIC ACID C10 H17 N3 O9 S QGWRMTHFAZVWAM-WDSKDSINSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.131 (Depositor), 0.138 (DCC) 
• R-Value Work:  0.114 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.115 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.664	α = 90
b = 54.217	β = 90
c = 55.147	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description