› 4k4d

X-ray diffraction
2.17Å resolution

X-ray crystal structure of E. coli YbdB complexed with 2,4-dihydroxyphenacyl-CoA

Released:
DOI: 10.2210/pdb4k4d/pdb
PDB entry 4k4d coloured by chain, front view.
PDB entry 4k4d coloured by chain, side view.
PDB entry 4k4d coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structure and catalysis in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB.
Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D
OpenAccess logo Biochemistry 53 4788-805 (2014)
PMID: 25010423

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-141755 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Proofreading thioesterase EntH Chains: A, B
Molecule details ›
Chains: A, B
Length: 137 amino acids
Theoretical weight: 14.99 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8Y8 (Residues: 1-137; Coverage: 100%)
Gene names: JW0589, b0597, entH, ybdB
Sequence domains: Thioesterase superfamily
Structure domains: Hotdog Thioesterase

Ligands and Environments

3 bound ligands:
Ligand HFQ 2 x HFQ
Ligand MLI 1 x MLI
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU300
Spacegroup: P21212
Unit cell:
a: 59.664Å b: 86.263Å c: 50.25Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.193 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Enzyme promiscuity: engine of evolutionary innovation.
Pandya et al. (2014)
7 other articles

2 mentions without citation

Structure and catalysis in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB.
Wu et al. (2014)
1 more