› 3vl2

X-ray diffraction
2.06Å resolution

3-isopropylmalate dehydrogenase from Shewanella oneidensis MR-1 at 160 MPa

Released:
DOI: 10.2210/pdb3vl2/pdb
PDB entry 3vl2 coloured by chain, front view.
PDB entry 3vl2 coloured by chain, side view.
PDB entry 3vl2 coloured by chain, top view.
Source organism: Shewanella oneidensis MR-1
Primary publication:
High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase.
Nagae T, Kawamura T, Chavas LM, Niwa K, Hasegawa M, Kato C, Watanabe N
Acta Crystallogr D Biol Crystallogr 68 300-9 (2012)
PMID: 22349232

Function and Biology Details

Reaction catalysed: 
(1a) (2R,3S)-3-isopropylmalate + NAD(+) = (2S)-2-isopropyl-3-oxosuccinate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184326 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-isopropylmalate dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 375 amino acids
Theoretical weight: 40.69 KDa
Source organism: Shewanella oneidensis MR-1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8E9N3 (Residues: 2-364; Coverage: 100%)
Gene names: SO_4235, leuB
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand IPM 1 x IPM
Ligand CA 1 x CA
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: C2
Unit cell:
a: 104.298Å b: 58.251Å c: 76.044Å
α: 90° β: 119.09° γ: 90°
R-values:
R R work R free
0.139 0.136 0.191
Expression system: Escherichia coli

Quick links

Citations

3 review citations

High-pressure macromolecular crystallography and NMR: status, achievements and prospects.
Fourme et al. (2012)
2 more

1 mention without citation

High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase.
Nagae et al. (2012)