3BBY | pdb_00003bby

Crystal structure of glutathione S-transferase (NP_416804.1) from Escherichia coli K12 at 1.85 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BBY/pdb

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


• Deposited: 2007-11-11 Released: 2007-11-20 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.195 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of glutathione S-transferase (NP_416804.1) from Escherichia coli K12 at 1.85 A resolution

Joint Center for Structural Genomics (JCSG)

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: 24.92 kDa 
• Atom Count: 1,800 
• Modeled Residue Count: 191 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized GST-like protein yfcF	A	215	Escherichia coli K-12	Mutation(s): 0  Gene Names: yfcF, b2301, JW2298 EC: 2.5.1.18
UniProt
Find proteins for P77544 (Escherichia coli (strain K12)) Explore P77544  Go to UniProtKB:  P77544

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ETX	E [auth A], F [auth A]	2-ETHOXYETHANOL C4 H10 O2 ZNQVEEAIQZEUHB-UHFFFAOYSA-N
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.195 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33BBY

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.96	α = 90
b = 69.96	β = 90
c = 92.02	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary