3CA9 | pdb_00003ca9

Evolution of chlorella virus dUTPase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.307 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

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This is version 1.2 of the entry. See complete history. 

Literature

Crystallization and crystal-packing studies of Chlorella virus deoxyuridine triphosphatase.

Homma, K., Moriyama, H.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1030-1034

  • DOI: https://doi.org/10.1107/S1744309109034459
  • Primary Citation Related Structures: 
    3C2T, 3C3I, 3CA9

  • PubMed Abstract: 

    The 141-amino-acid deoxyuridine triphosphatase (dUTPase) from the algal Chlorella virus IL-3A and its Glu81Ser/Thr84Arg-mutant derivative Mu-22 were crystallized using the hanging-drop vapor-diffusion method at 298 K with polyethylene glycol as the precipitant. An apo IL-3A dUTPase with an amino-terminal T7 epitope tag and a carboxy-terminal histidine tag yielded cubic P2(1)3 crystals with unit-cell parameter a = 106.65 A. In the presence of dUDP, the enzyme produced thin stacked orthorhombic P222 crystals with unit-cell parameters a = 81.0, b = 96.2, c = 132.8 A. T7-histidine-tagged Mu-22 dUTPase formed thin stacked rectangular crystals. Amino-terminal histidine-tagged dUTPases did not crystallize but formed aggregates. Glycyl-seryl-tagged dUTPases yielded cubic P2(1)3 IL-3A crystals with unit-cell parameter a = 105.68 A and hexagonal P6(3) Mu-22 crystals with unit-cell parameters a = 132.07, c = 53.45 A, gamma = 120 degrees . Owing to the Thr84Arg mutation, Mu-22 dUTPase had different monomer-to-monomer interactions to those of IL-3A dUTPase.

    • Organizational Affiliation: 
    • Department of Chemistry, University of Nebraska-Lincoln, NE 68583-0304, USA.

Macromolecule Content 

  • Total Structure Weight: 35.9 kDa 
  • Atom Count: 1,976 
  • Modeled Residue Count: 254 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Deoxyuridine triphosphatase
A, B
165Paramecium bursaria Chlorella virus IL3AMutation(s): 0 
EC: 3.6.1.23
UniProt
Find proteins for Q5I3E5 (Paramecium bursaria Chlorella virus IL3A)
Explore Q5I3E5 
Go to UniProtKB:  Q5I3E5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5I3E5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.307 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.647α = 90
b = 105.647β = 90
c = 105.647γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations