› 3b06

X-ray diffraction
2.29Å resolution

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and DMAPP.

Released:
DOI: 10.2210/pdb3b06/pdb
PDB entry 3b06 coloured by chain, front view.
PDB entry 3b06 coloured by chain, side view.
PDB entry 3b06 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


Cofactor: Ligand FNR 4 x FNR
2 bound ligands:
Ligand DMA 4 x DMA
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P43212
Unit cell:
a: 100.842Å b: 100.842Å c: 334.499Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.239
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

Re-engaging cross-reactive memory B cells: the influenza puzzle.
Ellebedy et al. (2012)
1 more