4MK3 | pdb_00004mk3

Crystal structure of a glutathione transferase family member from Cupriavidus metallidurans CH34, target EFI-507362, with bound glutathione sulfinic acid (gso2h)

• PDB DOI: https://doi.org/10.2210/pdb4MK3/pdb

• Classification: TRANSFERASE
• Organism(s): Cupriavidus metallidurans CH34
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-04 Released: 2013-09-18 
• Deposition Author(s): Toro, R., Bhosle, R., Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.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: 1.50 Å
• R-Value Free: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a glutathione transferase family member from Cupriavidus metallidurans CH34, target EFI-507362, with bound glutathione sulfinic acid (gso2h)

Toro, R., Bhosle, R., Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Armstrong, R.N., Almo, S.C.

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: 26.41 kDa 
• Atom Count: 1,926 
• Modeled Residue Count: 203 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A	226	Cupriavidus metallidurans CH34	Mutation(s): 0  Gene Names: gst-1, Rmet_2957 EC: 2.5.1.18
UniProt
Find proteins for Q1LJ46 (Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)) Explore Q1LJ46  Go to UniProtKB:  Q1LJ46

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSF	E [auth A]	L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE C10 H17 N3 O8 S DMAPAHUEYHXRFI-WDSKDSINSA-N
PG4	C [auth A], D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.611	α = 90
b = 70.611	β = 90
c = 89.553	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-3000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Toro, R., Bhosle, R., Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description