5XN8

Structure of glycerol dehydrogenase crystallised as a contaminant

• PDB DOI: https://doi.org/10.2210/pdb5XN8/pdb
• Entry: 5XN8 supersedes: 5WQ5

• Classification: OXIDOREDUCTASE
• Organism(s): unidentified
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-19 Released: 2017-06-07 
• Deposition Author(s): Hatti, K., Mathiharan, Y.K., Srinivasan, N., Murthy, M.R.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.251 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Literature

Seeing but not believing: the structure of glycerol dehydrogenase initially assumed to be the structure of a survival protein from Salmonella typhimurium

Hatti, K., Mathiharan, Y.K., Srinivasan, N., Murthy, M.R.N.

(2017) Acta Crystallogr D Biol Crystallogr 73: 609-617

• DOI: https://doi.org/10.1107/S2059798317007677

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 156.34 kDa 
• Atom Count: 11,128 
• Modelled Residue Count: 1,460 
• Deposited Residue Count: 1,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol Dehydrogenase	A, B, C, D	365	unidentified	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], I [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A], G [auth B], H [auth C], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.251 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.55	α = 90
b = 178.55	β = 90
c = 80.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data processing
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Hatti, K., Mathiharan, Y.K., Srinivasan, N., Murthy, M.R.N.
• This entry supersedes: 5WQ5

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Database references, Structure summary
• Version 1.2: 2017-08-16
  Changes: Database references
• Version 1.3: 2018-09-05
  Changes: Data collection, Database references
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description