4J0E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 

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 69: 515-519

  • DOI: 10.1107/S1744309113007045
  • Primary Citation of Related Structures:  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 elega ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable 3-hydroxyacyl-CoA dehydrogenase F54C8.1
A, B
320Caenorhabditis elegansEC: 1.1.1.35
Find proteins for P34439 (Caenorhabditis elegans)
Go to UniProtKB:  P34439
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.223 
  • 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
PHASESphasing
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references