› 5hn6

X-ray diffraction
2.5Å resolution

Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and 3-isopropylmalate

Released:
DOI: 10.2210/pdb5hn6/pdb
PDB entry 5hn6 coloured by chain, front view.
PDB entry 5hn6 coloured by chain, side view.
PDB entry 5hn6 coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Structure and function of an ancestral-type β-decarboxylating dehydrogenase from Thermococcus kodakarensis.
Shimizu T, Yin L, Yoshida A, Yokooji Y, Hachisuka SI, Sato T, Tomita T, Nishida H, Atomi H, Kuzuyama T, Nishiyama M
Biochem J 474 105-122 (2017)
PMID: 27831491

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177289 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isopropylmalate dehydrogenase-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 353 amino acids
Theoretical weight: 38.64 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JFV8 (Residues: 1-347; Coverage: 100%)
Gene name: TK0280
Sequence domains: Isocitrate/isopropylmalate dehydrogenase
Structure domains: Isopropylmalate Dehydrogenase

Ligands and Environments

3 bound ligands:
Ligand IPM 1 x IPM
Ligand MN 1 x MN
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P4322
Unit cell:
a: 80.161Å b: 80.161Å c: 142.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.199 0.251
Expression system: Escherichia coli

Quick links

Citations

1 review citation

An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research.
Rashid et al. (2020)
3 other articles