6JZL

S-formylglutathione hydrolase homolog from a psychrophilic bacterium of Shewanella frigidimarina

• PDB DOI: https://doi.org/10.2210/pdb6JZL/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella frigidimarina
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-02 Released: 2019-09-04 
• Deposition Author(s): Lee, C.W., Lee, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.235 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 

Literature

Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium.

Lee, C.W., Yoo, W., Park, S.H., Le, L.T.H.L., Jeong, C.S., Ryu, B.H., Shin, S.C., Kim, H.W., Park, H., Kim, K.K., Kim, T.D., Lee, J.H.

(2019) Microb Cell Fact 18: 140-140

• PubMed: 31426813 
• DOI: https://doi.org/10.1186/s12934-019-1190-1
• Primary Citation of Related Structures:  
  6JZL


• PubMed Abstract: 
  

  S-Formylglutathione is hydrolyzed to glutathione and formate by an S-formylglutathione hydrolase (SFGH) (3.1.2.12). This thiol esterase belongs to the esterase family and is also known as esterase D. SFGHs contain highly conserved active residues of Ser-Asp-His as a catalytic triad at the active site. Characterization and investigation of SFGH from Antarctic organisms at the molecular level is needed for industrial use through protein engineering.

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Organizational Affiliation: 

Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62.13 kDa 
• Atom Count: 4,549 
• Modelled Residue Count: 554 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-formylglutathione hydrolase	A, B	279	Shewanella frigidimarina	Mutation(s): 0  EC: 3.1.2.12
UniProt
Find proteins for Q07XK4 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q07XK4  Go to UniProtKB:  Q07XK4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.235 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.356	α = 90
b = 76.594	β = 105.32
c = 64.725	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MxDC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-04 
Deposition Author(s): Lee, C.W., Lee, J.H.

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references