2FNO

Crystal structure of a glutathione s-transferase (atu5508) from agrobacterium tumefaciens str. c58 at 2.00 A resolution

• PDB DOI:  https://doi.org/10.2210/pdb2FNO/pdb
• Entry: 2FNO supersedes: 1ZGM

• Classification: TRANSFERASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-01-11 Released: 2006-02-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.219 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Comparative structural analysis of a novel glutathioneS-transferase (ATU5508) from Agrobacterium tumefaciens at 2.0 A resolution.

Kosloff, M., Han, G.W., Krishna, S.S., Schwarzenbacher, R., Fasnacht, M., Elsliger, M.A., Abdubek, P., Agarwalla, S., Ambing, E., Astakhova, T., Axelrod, H.L., Canaves, J.M., Carlton, D., Chiu, H.J., Clayton, T., DiDonato, M., Duan, L., Feuerhelm, J., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Haugen, J., Jaroszewski, L., Jin, K.K., Johnson, H., Klock, H.E., Knuth, M.W., Koesema, E., Kreusch, A., Kuhn, P., Levin, I., McMullan, D., Miller, M.D., Morse, A.T., Moy, K., Nigoghossian, E., Okach, L., Oommachen, S., Page, R., Paulsen, J., Quijano, K., Reyes, R., Rife, C.L., Sims, E., Spraggon, G., Sridhar, V., Stevens, R.C., van den Bedem, H., Velasquez, J., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2006) Proteins 65: 527-537

• PubMed: 16988933 
• DOI: https://doi.org/10.1002/prot.21130
• Primary Citation of Related Structures:  
  2FNO


• PubMed Abstract: 
  

Glutathione S-transferases (GSTs) comprise a diverse superfamily of enzymes found in organisms from all kingdoms of life. GSTs are involved in diverse processes, notably small-molecule biosynthesis or detoxification, and are frequently also used in protein engineering studies or as biotechnology tools. Here, we report the high-resolution X-ray structure of Atu5508 from the pathogenic soil bacterium Agrobacterium tumefaciens (atGST1). Through use of comparative sequence and structural analysis of the GST superfamily, we identified local sequence and structural signatures, which allowed us to distinguish between different GST classes. This approach enables GST classification based on structure, without requiring additional biochemical or immunological data. Consequently, analysis of the atGST1 crystal structure suggests a new GST class, distinct from previously characterized GSTs, which would make it an attractive target for further biochemical studies.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 56.03 kDa 
• Atom Count: 4,028 
• Modelled Residue Count: 473 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_pAT_752p	A, B	248	Agrobacterium fabrum str. C58	Mutation(s): 7  Gene Names: 15162326, gst, Atu5508
UniProt
Find proteins for Q7D2W7 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7D2W7  Go to UniProtKB:  Q7D2W7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SCN	C [auth A], D [auth A], E [auth B], F [auth B]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.219 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M32FNO

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.204	α = 90
b = 50.261	β = 115.72
c = 117.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 1ZGM

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations