3SO2 | pdb_00003so2

Chlorella dUTPase

• PDB DOI: https://doi.org/10.2210/pdb3SO2/pdb

• Classification: HYDROLASE
• Organism(s): Chlorella variabilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-29 Released: 2012-07-04 
• Deposition Author(s): Badalucco, L., Poudel, I., Natarajan, c., Yamanishi, M., Moriyama, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

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

• PubMed: 22139176 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.38 kDa 
• Atom Count: 1,143 
• Modelled Residue Count: 137 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A	146	Chlorella variabilis	Mutation(s): 0  Gene Names: CHLNCDRAFT_27939 EC: 3.6.1.23
UniProt
Find proteins for E1ZRW6 (Chlorella variabilis) Explore E1ZRW6  Go to UniProtKB:  E1ZRW6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.91	α = 90
b = 66.91	β = 90
c = 93.63	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-04 
Deposition Author(s): Badalucco, L., Poudel, I., Natarajan, c., Yamanishi, M., Moriyama, H.

Revision History  

• 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