› 2itb

X-ray diffraction
2.05Å resolution

CRYSTAL STRUCTURE OF A PUTATIVE TRNA-(MS(2)IO(6)A)-HYDROXYLASE (PP_2188) FROM PSEUDOMONAS PUTIDA KT2440 AT 2.05 A RESOLUTION

Released:
DOI: 10.2210/pdb2itb/pdb
PDB entry 2itb coloured by chain, front view.
PDB entry 2itb coloured by chain, side view.
PDB entry 2itb coloured by chain, top view.
Source organism: Pseudomonas putida KT2440
Entry author: Joint Center for Structural Genomics (JCSG)

Function and Biology Details

Reaction catalysed: 
2-(methylsulfanyl)-N(6)-prenyladenosine(37) in tRNA + reduced acceptor + O(2) = N(6)-((2E)-4-hydroxy-3-methylbut-2-en-1-yl)-2-(methylsulfanyl)adenosine(37) in tRNA + acceptor + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183488 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA 2-(methylsulfanyl)-N(6)-isopentenyladenosine(37) hydroxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 206 amino acids
Theoretical weight: 23.36 KDa
Source organism: Pseudomonas putida KT2440
Expression system: Escherichia coli
UniProt:
  • Canonical: Q88KV1 (Residues: 1-205; Coverage: 100%)
Gene names: PP_2188, miaE
Sequence domains: tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
Structure domains: Ferritin

Ligands and Environments

4 bound ligands:
Ligand FE 4 x FE
Ligand PER 1 x PER
Ligand EDO 17 x EDO
Ligand UNL 1 x UNL
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 61.274Å b: 70.215Å c: 84.285Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.171 0.229
Expression system: Escherichia coli

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