› 3rk1

X-ray diffraction
2.3Å resolution

'X-ray crystal Structure of the putative N-type ATP pyrophosphatase (PF0828) in complex with ATP from Pyrococcus furiosus, Northeast Structural Genomics Consortium Target PfR23

Released:
DOI: 10.2210/pdb3rk1/pdb
PDB entry 3rk1 coloured by chain, front view.
PDB entry 3rk1 coloured by chain, side view.
PDB entry 3rk1 coloured by chain, top view.
Source organism: Pyrococcus furiosus DSM 3638
Primary publication:
A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding.
Forouhar F, Saadat N, Hussain M, Seetharaman J, Lee I, Janjua H, Xiao R, Shastry R, Acton TB, Montelione GT, Tong L
Acta Crystallogr Sect F Struct Biol Cryst Commun 67 1323-7 (2011)
PMID: 22102225

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186445 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diphthamide synthase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 237 amino acids
Theoretical weight: 27.11 KDa
Source organism: Pyrococcus furiosus DSM 3638
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8U2K6 (Residues: 1-229; Coverage: 100%)
Gene name: PF0828
Sequence domains: Diphthamide synthase
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ATP 2 x ATP
Ligand PO4 3 x PO4
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P212121
Unit cell:
a: 58.979Å b: 64.072Å c: 140.134Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.203 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

A structural perspective on the PP-loop ATP pyrophosphatase family.
Fellner et al. (2018)
1 other article

5 mentions without citation

Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage.
de Crécy-Lagard et al. (2012)
4 more