3R2Q | pdb_00003r2q

Crystal Structure Analysis of yibF from E. Coli

• PDB DOI: https://doi.org/10.2210/pdb3R2Q/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-14 Released: 2012-03-14 
• Deposition Author(s): Ladner, J.E., Harp, J., Schaab, M., Stournan, N.V., Armstrong, R.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.153 (Depositor), 0.157 (DCC) 
• R-Value Work: 
  0.139 (DCC) 

Literature

Structural and Functional Genomics of YibF, a Glutathione Transferase Homologue from Escherichia coli

Ladner, J.E., Stournan, N.V., Branch, M.C., Harp, J., Schaab, M., Brown, D.W., Armstrong, R.N.

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: 23.11 kDa 
• Atom Count: 2,079 
• Modeled Residue Count: 202 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized GST-like protein yibF	A	202	Escherichia coli K-12	Mutation(s): 0  Gene Names: b3592, JW3565, yibF
UniProt
Find proteins for P0ACA1 (Escherichia coli (strain K12)) Explore P0ACA1  Go to UniProtKB:  P0ACA1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free:  0.153 (Depositor), 0.157 (DCC) 
• R-Value Work:  0.139 (DCC) 

Space Group: P 4₃ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.34	α = 90
b = 111.34	β = 90
c = 111.34	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
SHELX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
ARP/wARP	model building
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Ladner, J.E., Harp, J., Schaab, M., Stournan, N.V., Armstrong, R.N.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary