› 2idb

X-ray diffraction
2.9Å resolution

Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.

Released:
DOI: 10.2210/pdb2idb/pdb
PDB entry 2idb coloured by chain, front view.
PDB entry 2idb coloured by chain, side view.
PDB entry 2idb coloured by chain, top view.
Source organism: Escherichia coli K-12
Entry authors: Zhou W, Forouhar F, Seetharaman J, Fang Y, Xiao R, Cunningham K, Ma L-C, Chen CX, Acton TB, Montelione GT, Hunt JF, Tong L, Northeast Structural Genomics Consortium (NESG)

Function and Biology Details

Reaction catalysed: 
A 4-hydroxy-3-polyprenylbenzoate = a 2-polyprenylphenol + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141980 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
3-octaprenyl-4-hydroxybenzoate carboxy-lyase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 505 amino acids
Theoretical weight: 57.35 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AAB4 (Residues: 1-497; Coverage: 100%)
Gene names: JW3819, b3843, ubiD, yigC, yigY
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 1PE 3 x 1PE
Ligand EDO 3 x EDO
1 modified residue:
Ligand MSE 39 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X4A
Spacegroup: P43212
Unit cell:
a: 194.295Å b: 194.295Å c: 106.051Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.201 0.265
Expression system: Escherichia coli

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