› 3d3q

X-ray diffraction
2.7Å resolution

Crystal structure of tRNA delta(2)-isopentenylpyrophosphate transferase (SE0981) from Staphylococcus epidermidis. Northeast Structural Genomics Consortium target SeR100

Released:
DOI: 10.2210/pdb3d3q/pdb
PDB entry 3d3q coloured by chain, front view.
PDB entry 3d3q coloured by chain, side view.
PDB entry 3d3q coloured by chain, top view.
Source organism: Staphylococcus epidermidis ATCC 12228
Entry authors: Forouhar F, Abashidze M, Seetharaman J, Mao L, Xiao R, Maglaqui M, Lee D, Everett JK, Acton TB, Montelione GT, Tong L, Hunt JF, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Reaction catalysed: 
Dimethylallyl diphosphate + adenine(37) in tRNA = diphosphate + N(6)-(3-methylbut-2-en-1-yl)-adenine(37) in tRNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184004 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
tRNA dimethylallyltransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 340 amino acids
Theoretical weight: 40.36 KDa
Source organism: Staphylococcus epidermidis ATCC 12228
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8CQL3 (Residues: 1-332; Coverage: 100%)
Gene names: SE_0981, miaA
Sequence domains: IPP transferase
Structure domains:

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 30 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4C
Spacegroup: P21
Unit cell:
a: 58.622Å b: 84.48Å c: 75.397Å
α: 90° β: 102.87° γ: 90°
R-values:
R R work R free
0.232 0.231 0.271
Expression system: Escherichia coli

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