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X-ray diffraction
1.8Å resolution

CRYSTAL STRUCTURE OF NUDIX HYDROLASE DR1025 IN COMPLEX WITH SM+3

Released:
DOI: 10.2210/pdb1soi/pdb
PDB entry 1soi coloured by chain, front view.
PDB entry 1soi coloured by chain, side view.
PDB entry 1soi coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Structural studies of the Nudix hydrolase DR1025 from Deinococcus radiodurans and its ligand complexes.
Ranatunga W, Hill EE, Mooster JL, Holbrook EL, Schulze-Gahmen U, Xu W, Bessman MJ, Brenner SE, Holbrook SR
J Mol Biol 339 103-16 (2004)
PMID: 15123424

Function and Biology Details

Reactions catalysed: 
P(1),P(4)-bis(5'-adenosyl)tetraphosphate + H(2)O = ATP + AMP
8-oxo-GTP + H(2)O = 8-oxo-GDP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193302 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase DR_1025 Chain: A
Molecule details ›
Chain: A
Length: 159 amino acids
Theoretical weight: 17.59 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RVK2 (Residues: 1-159; Coverage: 100%)
Gene name: DR_1025
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

1 bound ligand:
Ligand SM 3 x SM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P41212
Unit cell:
a: 53.171Å b: 53.171Å c: 121.972Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.218 0.251
Expression system: Escherichia coli

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Citations

1 review citation

Structures and mechanisms of Nudix hydrolases.
Mildvan et al. (2005)
16 other articles