4G9H

Crystal structure of glutahtione s-transferase homolog from yersinia pestis, target EFI-501894, with bound glutathione

• PDB DOI: https://doi.org/10.2210/pdb4G9H/pdb

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


• Deposited: 2012-07-23 Released: 2012-08-15 
• Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

Crystal structure of glutahtione s-transferase homolog from yersinia pestis, target efi-501894, with bound glutathione

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., 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: 48.29 kDa 
• Atom Count: 3,557 
• Modelled Residue Count: 404 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A, B	211	Yersinia pestis	Mutation(s): 0  Gene Names: gst, gst2, y1968, YP_2153
UniProt
Find proteins for Q8D0L3 (Yersinia pestis) Explore Q8D0L3  Go to UniProtKB:  Q8D0L3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	C [auth A], E [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.216 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.945	α = 90
b = 87.945	β = 90
c = 148.786	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description