4J0E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1107/S1744309113007045
  • Primary Citation of Related Structures:  
    4J0E, 4J0F

  • PubMed Abstract: 
  • 3-Hydroxyacyl-CoA dehydrogenase (HAD; EC 1.1.1.35) 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 ...

    3-Hydroxyacyl-CoA dehydrogenase (HAD; EC 1.1.1.35) 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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable 3-hydroxyacyl-CoA dehydrogenase F54C8.1A, B320Caenorhabditis elegansMutation(s): 0 
Gene Names: F54C8.1
EC: 1.1.1.35
UniProt
Find proteins for P34439 (Caenorhabditis elegans)
Explore P34439 
Go to UniProtKB:  P34439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34439
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2013-01-30 
  • Released Date: 2014-03-19 
  • Deposition Author(s): Xu, Y., Sun, F., Zhai, Y.

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