3SO2

Chlorella dUTPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallization of Chlorella deoxyuridine triphosphatase.

Badalucco, L.Poudel, I.Yamanishi, M.Natarajan, C.Moriyama, H.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1599-1602

  • DOI: https://doi.org/10.1107/S1744309111038097
  • Primary Citation of Related Structures:  
    3SO2

  • PubMed Abstract: 

    Deoxyuridine triphosphatase (dUTPase) is a ubiquitous enzyme that has been widely studied owing to its function and evolutionary significance. The gene coding for the dUTPase from the Chlorella alga was codon-optimized and synthesized. The synthetic gene was expressed in Escherichia coli and recombinant core Chlorella dUTPase (chdUTPase) was purified. Crystallization of chdUTPase was performed by the repetitive hanging-drop vapor-diffusion method at 298 K with ammonium sulfate as the precipitant. In the presence of 2'-deoxyuridine-5'-[(α,β)-imido]triphosphate and magnesium, the enzyme produced die-shaped hexagonal R3 crystals with unit-cell parameters a = b = 66.9, c = 93.6 Å, γ = 120°. X-ray diffraction data for chdUTPase were collected to 1.6 Å resolution. The crystallization of chdUTPase with manganese resulted in very fragile clusters of needles.


  • Organizational Affiliation

    School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588-0118, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein146Chlorella variabilisMutation(s): 0 
Gene Names: CHLNCDRAFT_27939
EC: 3.6.1.23
UniProt
Find proteins for E1ZRW6 (Chlorella variabilis)
Explore E1ZRW6 
Go to UniProtKB:  E1ZRW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1ZRW6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.251 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.91α = 90
b = 66.91β = 90
c = 93.63γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description