› 3wjr

X-ray diffraction
1.86Å resolution

crystal structure of HypE in complex with a nucleotide

Released:
DOI: 10.2210/pdb3wjr/pdb
PDB entry 3wjr coloured by chain, front view.
PDB entry 3wjr coloured by chain, side view.
PDB entry 3wjr coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation.
Tominaga T, Watanabe S, Matsumi R, Atomi H, Imanaka T, Miki K
Proc Natl Acad Sci U S A 110 20485-90 (2013)
PMID: 24297906

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-177321 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hydrogenase expression/formation protein HypE Chain: A
Molecule details ›
Chain: A
Length: 338 amino acids
Theoretical weight: 35.95 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JII7 (Residues: 1-338; Coverage: 100%)
Gene name: TK1993
Sequence domains:
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand BEN 2 x BEN
Ligand AMP 1 x AMP
Ligand SO4 5 x SO4
Ligand PGE 1 x PGE
Ligand GOL 1 x GOL
Ligand PEG 1 x PEG
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P43212
Unit cell:
a: 102.657Å b: 102.657Å c: 105.728Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.173 0.2
Expression system: Escherichia coli

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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)
6 other articles

1 mention without citation

Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation.
Tominaga et al. (2013)