4O92 | pdb_00004o92

Crystal structure of a Glutathione S-transferase from Pichia kudriavzevii (Issatchenkia orientalis), target EFI-501747

• PDB DOI: https://doi.org/10.2210/pdb4O92/pdb

• Classification: TRANSFERASE
• Organism(s): Pichia kudriavzevii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-31 Released: 2014-01-15 
• Deposition Author(s): Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Attonito, J.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Crystal structure of a Glutathione S-transferase from Pichia kudriavzevii (Issatchenkia orientalis), target EFI-501747

Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Attonito, J.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.57 kDa 
• Atom Count: 1,538 
• Modeled Residue Count: 196 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A	206	Pichia kudriavzevii	Mutation(s): 0  Gene Names: GSTY-1, Q9Y727
UniProt
Find proteins for Q9Y727 (Pichia kudriavzevii) Explore Q9Y727  Go to UniProtKB:  Q9Y727

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.258 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.207	α = 90
b = 48.207	β = 90
c = 187.068	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AutoSol	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Attonito, J.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary