4ID0

Crystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target EFI-900011, with bound glutathione sulfinic acid (gso2h) and acetate

• PDB DOI: https://doi.org/10.2210/pdb4ID0/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas fluorescens PF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-11 Released: 2012-12-26 
• Deposition Author(s): Vetting, M.W., Sauder, J.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Burley, S.K., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.172 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Crystal structure of a glutathione transferase family member from Pseudomonas fluorescens Pf-5, target EFI-900011, with bound glutathione sulfinic acid (gso2h) and acetate

Vetting, M.W., Sauder, J.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Burley, S.K., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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: 49.49 kDa 
• Atom Count: 4,036 
• Modelled Residue Count: 408 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase-like protein YibF	A, B	214	Pseudomonas fluorescens PF5	Mutation(s): 0  Gene Names: yibF, PFL_5710
UniProt
Find proteins for Q4K4R5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K4R5  Go to UniProtKB:  Q4K4R5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSF	H [auth B]	L-GAMMA-GLUTAMYL-3-SULFINO-L-ALANYLGLYCINE C10 H17 N3 O8 S DMAPAHUEYHXRFI-WDSKDSINSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], D [auth A], E [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-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: 1.10 Å
• R-Value Free: 0.172 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.542	α = 90
b = 69.741	β = 90
c = 80.182	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Vetting, M.W., Sauder, J.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Burley, S.K., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-03-06
  Changes: Structure summary
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-12-06
  Changes: Data collection
• Version 1.6: 2024-10-09
  Changes: Structure summary