› 2pb4

X-ray diffraction
2.1Å resolution

Crystal structure of PH0725 from Pyrococcus horikoshii OT3

Released:
DOI: 10.2210/pdb2pb4/pdb
PDB entry 2pb4 coloured by chain, front view.
PDB entry 2pb4 coloured by chain, side view.
PDB entry 2pb4 coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Entry authors: Yamamoto H, Taketa M, Kageyama Y, 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: 29.62 KDa
Source organism: Pyrococcus horikoshii
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
1 bound ligand:
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P41212
Unit cell:
a: 104.786Å b: 104.786Å c: 139.742Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.236
Expression system: Escherichia coli

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