› 2vnq

X-ray diffraction
2.2Å resolution

Monoclinic form of IDI-1

Released:
DOI: 10.2210/pdb2vnq/pdb
PDB entry 2vnq coloured by chain, front view.
PDB entry 2vnq coloured by chain, side view.
PDB entry 2vnq coloured by chain, top view.
Source organism: Escherichia coli BL21
Primary publication:
Monoclinic form of isopentenyl diphosphate isomerase: a case of polymorphism in biomolecular crystals.
de Ruyck J, Oudjama Y, Wouters J
Acta Crystallogr Sect F Struct Biol Cryst Commun 64 239-42 (2008)
PMID: 18391416

Function and Biology Details

Reaction catalysed: 
Isopentenyl diphosphate = prenyl diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175138 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopentenyl-diphosphate Delta-isomerase Chains: A, B
Molecule details ›
Chains: A, B
Length: 183 amino acids
Theoretical weight: 20.64 KDa
Source organism: Escherichia coli BL21
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q46822 (Residues: 1-182; Coverage: 100%)
Gene names: JW2857, b2889, idi, ygfV
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

3 bound ligands:
Ligand MN 2 x MN
Ligand IMD 2 x IMD
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21
Unit cell:
a: 43.2Å b: 69.1Å c: 62.4Å
α: 90° β: 100.3° γ: 90°
R-values:
R R work R free
0.197 0.194 0.261
Expression system: Escherichia coli BL21

Quick links

Citations

1 citations in other articles

Crystallographic analysis of metal-ion binding to human ubiquitin.
Arnesano et al. (2011)

1 mention without citation

Monoclinic form of isopentenyl diphosphate isomerase: a case of polymorphism in biomolecular crystals.
de Ruyck et al. (2008)