2JGN

DDX3 helicase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Expression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Ddx3 RNA Helicase Domain.

Rodamilans, B.Montoya, G.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 283

  • DOI: https://doi.org/10.1107/S1744309107006434
  • Primary Citation of Related Structures:  
    2JGN

  • PubMed Abstract: 

    DDX3 is a human RNA helicase that is involved in RNA processing and important human diseases. This enzyme belongs to the DEAD-box protein family, the members of which are characterized by the presence of nine conserved motifs including the Asp-Glu-Ala-Asp motif that defines the family. DDX3 has two distinct domains: an ATP-binding domain in the central region of the protein and a helicase domain in the carboxy-terminal region. The helicase domain of DDX3 was cloned and overexpressed in Escherichia coli. Crystallization experiments yielded crystals that were suitable for X-ray diffraction analysis. The final crystallization conditions were a reservoir solution consisting of 2 M ammonium sulfate, 0.1 M imidazole pH 6.4 plus 5 mM spermine tetrahydrochloride and a protein solution containing 10 mM HEPES, 500 mM ammonium sulfate pH 8.0. The crystals of the helicase domain belong to the monoclinic space group P2(1), with unit-cell parameters a = 43.85, b = 60.72, c = 88.39 A, alpha = gamma = 90, beta = 101.02 degrees , and contained three molecules per asymmetric unit. These crystals diffracted to a resolution limit of 2.2 A using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS).


  • Organizational Affiliation

    Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO) Macromolecular Crystallography Group, c/Melchor Fdez Almagro 3, 28029 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-DEPENDENT RNA HELICASE DDX3X
A, B, C
185Homo sapiensMutation(s): 0 
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens)
Explore O00571 
Go to UniProtKB:  O00571
PHAROS:  O00571
GTEx:  ENSG00000215301 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00571
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.438α = 90
b = 61.032β = 101.67
c = 89.111γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-05-30
    Changes: Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description