6RZ0 | pdb_00006rz0

Crystal structure of Escherichia coli Glyoxalase II

• PDB DOI: https://doi.org/10.2210/pdb6RZ0/pdb

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


• Deposited: 2019-06-12 Released: 2020-07-15 
• Deposition Author(s): Skorupskaite, A., McDonough, M.A., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.128 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.119 (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: 29.11 kDa 
• Atom Count: 2,781 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	F [auth A]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], E [auth A], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.128 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.382	α = 90
b = 63.383	β = 90
c = 72.726	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

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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