› 2cv8

X-ray diffraction
2.8Å resolution

Crystal structure of tRNA-intron endonuclease from Sulfolobus tokodaii

Released:
DOI: 10.2210/pdb2cv8/pdb
PDB entry 2cv8 coloured by chain, front view.
PDB entry 2cv8 coloured by chain, side view.
PDB entry 2cv8 coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii
Entry authors: Kato-Murayama M, Bessho Y, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
PretRNA = a 3'-half-tRNA molecule with a 5'-OH end + a 5'-half-tRNA molecule with a 2',3'-cyclic phosphate end + an intron with a 2',3'-cyclic phosphate and a 5'-hydroxyl terminus
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-188846 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA-splicing endonuclease Chains: A, B
Molecule details ›
Chains: A, B
Length: 180 amino acids
Theoretical weight: 20.72 KDa
Source organism: Sulfurisphaera tokodaii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q975R3 (Residues: 1-180; Coverage: 100%)
Gene names: STK_03580, endA
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand CL 2 x CL
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1, SPRING-8 BEAMLINE BL41XU
Spacegroup: P43212
Unit cell:
a: 54.308Å b: 54.308Å c: 242.768Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.226 0.299
Expression system: Escherichia coli

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