› 5a60

X-ray diffraction
1.82Å resolution

Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two magnesium ions

Released:
DOI: 10.2210/pdb5a60/pdb
PDB entry 5a60 coloured by chain, front view.
PDB entry 5a60 coloured by chain, side view.
PDB entry 5a60 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.
Martinez J, Truffault V, Hothorn M
J Biol Chem 290 23348-60 (2015)
PMID: 26221030

Function and Biology Details

Reaction catalysed: 
Triphosphate + H(2)O = diphosphate + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151830 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Inorganic triphosphatase Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 48.64 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P30871 (Residues: 1-433; Coverage: 100%)
Gene names: JW3026, b3054, ygiF
Sequence domains: CYTH domain

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand 3PO 1 x 3PO
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P65
Unit cell:
a: 89.924Å b: 89.924Å c: 125.577Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.153 0.151 0.189
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

mRNA capping: biological functions and applications.
Ramanathan et al. (2016)
1 more

2 mentions without citation

Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes.
Martinez et al. (2015)
1 more