6S0I | pdb_00006s0i

Crystal structure of Escherichia coli Glyoxalase II with L-Tartrate in the active site

• PDB DOI: https://doi.org/10.2210/pdb6S0I/pdb

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


• Deposited: 2019-06-14 Released: 2020-07-15 
• Deposition Author(s): Skorupskaite, A., McDonough, M.A., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Escherichia coli Glyoxalase II

Skorupskaite, A., McDonough, M.A., Brem, J., Schofield, C.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: mass spectrometry, gel filtration

Macromolecule Content 

• Total Structure Weight: 28.99 kDa 
• Atom Count: 2,223 
• Modeled Residue Count: 251 
• Deposited Residue Count: 251 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyacylglutathione hydrolase GloB	A	251	Escherichia coli K-12	Mutation(s): 0  Gene Names: gloB, yafR, b0212, JW0202 EC: 3.1.2.6
UniProt
Find proteins for P0AC84 (Escherichia coli (strain K12)) Explore P0AC84  Go to UniProtKB:  P0AC84

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.053	α = 90
b = 43.655	β = 90
c = 159.067	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-15 
Deposition Author(s): Skorupskaite, A., McDonough, M.A., Schofield, C.J.

---

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M011224/1

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description