› 2dv5

X-ray diffraction
2.2Å resolution

Crystal structure of Leu65 to Ala mutant of Diphthine synthase

Released:
DOI: 10.2210/pdb2dv5/pdb
PDB entry 2dv5 coloured by chain, front view.
PDB entry 2dv5 coloured by chain, side view.
PDB entry 2dv5 coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Entry authors: Mizutani H, Matsuura Y, Kunishima N, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + 2-((3S)-3-carboxy-3-aminopropyl)-L-histidine-[translation elongation factor 2] = S-adenosyl-L-homocysteine + 2-((3S)-3-carboxy-3-(methylamino)propyl)-L-histidine-[translation elongation factor 2]
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-129728 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diphthine synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 265 amino acids
Theoretical weight: 29.57 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O58456 (Residues: 1-265; Coverage: 100%)
Gene names: PH0725, dph5, dphB
Sequence domains: Tetrapyrrole (Corrin/Porphyrin) Methylases
Structure domains:

Ligands and Environments


Cofactor: Ligand SAH 1 x SAH
3 bound ligands:
Ligand SO4 7 x SO4
Ligand MES 2 x MES
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P41212
Unit cell:
a: 105.219Å b: 105.219Å c: 137.334Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.228
Expression system: Escherichia coli

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