Crystal structure of 3-hydroxyacyl-CoA dehydrogenase from Caenorhadbitis elegans in P1 space group

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

Starting Model: experimental
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Purification, crystallization and preliminary crystallographic analysis of 3-hydroxyacyl-CoA dehydrogenase from Caenorhabditis elegans.

Xu, Y.Sun, F.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 515-519

  • DOI: https://doi.org/10.1107/S1744309113007045
  • Primary Citation of Related Structures:  
    4J0E, 4J0F

  • PubMed Abstract: 

    3-Hydroxyacyl-CoA dehydrogenase (HAD; EC is the enzyme that catalyzes the third step in fatty-acid β-oxidation, oxidizing the hydroxyl group of 3-hydroxyacyl-CoA to a keto group. The 3-hydroxyacyl-CoA dehydrogenase from Caenorhabditis elegans (cHAD) was cloned, overexpressed in Escherichia coli and purified to homogeneity for crystallography. Initial crystals were obtained by the hanging-drop vapour-diffusion method. Optimization of the precipitant concentration and the pH yielded two types of well diffracting crystals with parallelepiped and cuboid shapes, respectively. Complete diffraction data sets were collected and processed from both crystal types. Preliminary crystallographic analysis indicated that the parallelepiped-shaped crystal belonged to space group P1, while the cuboid-shaped crystal belonged to space group P212121. Analyses of computed Matthews coefficient and self-rotation functions suggested that there are two cHAD molecules in one asymmetric unit in both crystals, forming identical dimers but packing in distinct manners.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing 100101, PR China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable 3-hydroxyacyl-CoA dehydrogenase F54C8.1
A, B
320Caenorhabditis elegansMutation(s): 0 
Gene Names: F54C8.1
Find proteins for P34439 (Caenorhabditis elegans)
Explore P34439 
Go to UniProtKB:  P34439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34439
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.709α = 80.45
b = 55.215β = 75.58
c = 56.066γ = 72.42
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description