› 6f2h

X-ray diffraction
2.19Å resolution

Structure of Protease 1 from Pyrococcus horikoshii co-crystallized in presence of 10 mM Tb-Xo4 and potassium iodide.

Released:
DOI: 10.2210/pdb6f2h/pdb
PDB entry 6f2h coloured by chain, front view.
PDB entry 6f2h coloured by chain, side view.
PDB entry 6f2h coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography.
Engilberge S, Riobé F, Wagner T, Di Pietro S, Breyton C, Franzetti B, Shima S, Girard E, Dumont E, Maury O
Chemistry 24 9739-9746 (2018)
PMID: 29806881

Function and Biology Details

Reaction catalysed: 
An N(6)-(1-hydroxy-2-oxopropyl)-[protein]-L-lysine + H(2)O = a [protein]-L-lysine + lactate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129858 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deglycase PH1704 Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 166 amino acids
Theoretical weight: 18.65 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O59413 (Residues: 1-166; Coverage: 100%)
Gene name: PH1704
Sequence domains: DJ-1/PfpI family
Structure domains: Rossmann fold

Ligands and Environments

3 bound ligands:
Ligand 7MT 9 x 7MT
Ligand IOD 11 x IOD
Ligand TB 9 x TB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21
Unit cell:
a: 82.577Å b: 84.698Å c: 144.343Å
α: 90° β: 90.97° γ: 90°
R-values:
R R work R free
0.152 0.15 0.193
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

NMR Spectroscopy of supramolecular chemistry on protein surfaces.
Bayer et al. (2020)
1 other article

1 mention without citation

Codon insertion and deletion functions as a somatic diversification mechanism in human antibody repertoires.
Reason et al. (2006)