2PC5 | pdb_00002pc5

Native crystal structure analysis on Arabidopsis dUTPase

• PDB DOI: https://doi.org/10.2210/pdb2PC5/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-03-29 Released: 2008-02-12 
• Deposition Author(s): Moriyama, H., Bajaj, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Purification, crystallization and preliminary crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Arabidopsis thaliana.

Bajaj, M., Moriyama, H.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 409-411

• PubMed: 17565183 
• DOI: https://doi.org/10.1107/S1744309107016004
• Primary Citation Related Structures: 
  2PC5


• PubMed Abstract: 
  

  The deoxyuridine triphosphate nucleotidohydrolase gene from Arabidopsis thaliana was expressed and the gene product was purified. Crystallization was performed by the hanging-drop vapour-diffusion method at 298 K using 2 M ammonium sulfate as the precipitant. X-ray diffraction data were collected to 2.2 A resolution using Cu K alpha radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 69.90, b = 70.86 A, c = 75.55 A. Assuming the presence of a trimer in the asymmetric unit, the solvent content was 30%, with a V(M) of 1.8 A3 Da(-1).

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Organizational Affiliation: 
• School of Biological Sciences, University of Nebraska-Lincoln, Manter Hall, Lincoln, Nebraska 68588-0304, 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 53.61 kDa 
• Atom Count: 3,078 
• Modeled Residue Count: 380 
• Deposited Residue Count: 507 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUTP pyrophosphatase-like protein	A, B, C	169	Arabidopsis thaliana	Mutation(s): 0  Gene Names: T6H20.30 EC: 3.6.1.23
UniProt
Find proteins for Q9STG6 (Arabidopsis thaliana) Explore Q9STG6  Go to UniProtKB:  Q9STG6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.251 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.903	α = 90
b = 70.86	β = 90
c = 75.555	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Moriyama, H., Bajaj, M.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description