› 3ajd

X-ray diffraction
1.27Å resolution

Crystal structure of ATRM4

Released:
DOI: 10.2210/pdb3ajd/pdb
PDB entry 3ajd coloured by chain, front view.
PDB entry 3ajd coloured by chain, side view.
PDB entry 3ajd coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii
Primary publication:
Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.
Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine S, Bessho Y, Ito T, Grosjean H, Yokoyama S
J Mol Biol 401 323-33 (2010)
PMID: 20600111

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178767 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA (cytosine(48)-C(5))-methyltransferase Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 31.54 KDa
Source organism: Methanocaldococcus jannaschii
Expression system: Escherichia coli
UniProt:
  • Canonical: Q60343 (Residues: 1-274; Coverage: 100%)
Gene names: MJ0026, trm4
Sequence domains: 16S rRNA methyltransferase RsmB/F
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand IPA 1 x IPA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 40.128Å b: 40.108Å c: 90.559Å
α: 90° β: 102.75° γ: 90°
R-values:
R R work R free
0.169 0.168 0.185
Expression system: Escherichia coli

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Citations

2 review citations

Methylated nucleosides in tRNA and tRNA methyltransferases.
Hori H. (2014)
1 more