4MF6 | pdb_00004mf6

Crystal structure of glutathione transferase BgramDRAFT_1843 from Burkholderia graminis, Target EFI-507289, with two glutathione molecules bound per one protein subunit

• PDB DOI: https://doi.org/10.2210/pdb4MF6/pdb

• Classification: TRANSFERASE
• Organism(s): Paraburkholderia graminis C4D1M
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-27 Released: 2013-09-04 
• Deposition Author(s): Patskovsky, Y., Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., 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: 1.20 Å
• R-Value Free: 
  0.131 (Depositor), 0.135 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.114 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glutathione transferase BgramDRAFT_1843 from Burkholderia graminis, Target EFI-507289, with two glutathione molecules bound per one protein subunit

Patskovsky, Y., Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., 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: 29.57 kDa 
• Atom Count: 2,366 
• Modeled Residue Count: 240 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase domain	A	256	Paraburkholderia graminis C4D1M	Mutation(s): 0  Gene Names: BgramDRAFT_1843 EC: 2.5.1.18
UniProt
Find proteins for B1FXZ2 (Paraburkholderia graminis (strain ATCC 700544 / DSM 17151 / LMG 18924 / NCIMB 13744 / C4D1M)) Explore B1FXZ2  Go to UniProtKB:  B1FXZ2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A], C [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
BEZ	D [auth A]	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	B [auth A], C [auth A]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free:  0.131 (Depositor), 0.135 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.114 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.175	α = 90
b = 84.175	β = 90
c = 78.597	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: 2013-09-04 
Deposition Author(s): Patskovsky, Y., Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., 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: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description