› 3b04

X-ray diffraction
2.3Å resolution

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with oIPP.

Released:
DOI: 10.2210/pdb3b04/pdb
PDB entry 3b04 coloured by chain, front view.
PDB entry 3b04 coloured by chain, side view.
PDB entry 3b04 coloured by chain, top view.
Source organism: Saccharolobus shibatae
Primary publication:
Covalent modification of reduced flavin mononucleotide in type-2 isopentenyl diphosphate isomerase by active-site-directed inhibitors.
Nagai T, Unno H, Janczak MW, Yoshimura T, Poulter CD, Hemmi H
Proc Natl Acad Sci U S A 108 20461-6 (2011)
PMID: 22158896

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158301 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopentenyl-diphosphate delta-isomerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 368 amino acids
Theoretical weight: 40.48 KDa
Source organism: Saccharolobus shibatae
Expression system: Escherichia coli
UniProt:
  • Canonical: P61615 (Residues: 1-368; Coverage: 100%)
Gene names: J5U23_00185, fni, idi
Sequence domains: FMN-dependent dehydrogenase
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand OOP 4 x OOP
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P43212
Unit cell:
a: 101.234Å b: 101.234Å c: 337.42Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.186 0.22
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Mechanistic aspects of carotenoid biosynthesis.
Moise et al. (2014)
3 more

2 mentions without citation

A relaxed active site after exon ligation by the group I intron.
Lipchock et al. (2008)
1 more