› 3ahe

X-ray diffraction
2.1Å resolution

Phosphoketolase from Bifidobacterium Breve complexed with dihydroxyethyl thiamine diphosphate

Released:
DOI: 10.2210/pdb3ahe/pdb
PDB entry 3ahe coloured by chain, front view.
PDB entry 3ahe coloured by chain, side view.
PDB entry 3ahe coloured by chain, top view.
Source organism: Bifidobacterium breve
Primary publication:
Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism.
Suzuki R, Katayama T, Kim BJ, Wakagi T, Shoun H, Ashida H, Yamamoto K, Fushinobu S
J Biol Chem 285 34279-87 (2010)
PMID: 20739284

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112791 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Probable phosphoketolase Chain: A
Molecule details ›
Chain: A
Length: 845 amino acids
Theoretical weight: 94.96 KDa
Source organism: Bifidobacterium breve
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D6PAH1 (Residues: 1-825; Coverage: 100%)
Gene name: xfp
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MG 1 x MG
Ligand THD 1 x THD
Ligand NA 1 x NA
Ligand EDO 11 x EDO
Ligand 2PE 1 x 2PE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: I422
Unit cell:
a: 173.529Å b: 173.529Å c: 163.516Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.161 0.206
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

CC bond formation using ThDP-dependent lyases.
Müller et al. (2013)
1 more

4 mentions without citation

Structure and evolution of the bifidobacterial carbohydrate metabolism proteins and enzymes.
Fushinobu et al. (2021)
3 more