› 3i8b

X-ray diffraction
2Å resolution

The crystal structure of xylulose kinase from Bifidobacterium adolescentis

Released:
DOI: 10.2210/pdb3i8b/pdb
PDB entry 3i8b coloured by chain, front view.
PDB entry 3i8b coloured by chain, side view.
PDB entry 3i8b coloured by chain, top view.
Source organism: Bifidobacterium adolescentis ATCC 15703
Entry authors: Zhang Z, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reaction catalysed: 
ATP + D-xylulose = ADP + D-xylulose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-106530 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xylulose kinase Chain: A
Molecule details ›
Chain: A
Length: 515 amino acids
Theoretical weight: 54.23 KDa
Source organism: Bifidobacterium adolescentis ATCC 15703
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1A0I0 (Residues: 3-506; Coverage: 100%)
Gene names: BAD_0432, xylB
Sequence domains:
Structure domains: Nucleotidyltransferase; domain 5

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: C2
Unit cell:
a: 96.732Å b: 61.918Å c: 94.606Å
α: 90° β: 93.04° γ: 90°
R-values:
R R work R free
0.183 0.18 0.226
Expression system: Escherichia coli BL21(DE3)

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