› 3zkk

X-ray diffraction
2.2Å resolution

Structure of the xylo-oligosaccharide specific solute binding protein from Bifidobacterium animalis subsp. lactis Bl-04 in complex with xylotetraose

Released:
DOI: 10.2210/pdb3zkk/pdb
PDB entry 3zkk coloured by chain, front view.
PDB entry 3zkk coloured by chain, side view.
PDB entry 3zkk coloured by chain, top view.
Source organism: Bifidobacterium animalis subsp. lactis Bl-04
Primary publication:
Structural basis for arabinoxylo-oligosaccharide capture by the probiotic Bifidobacterium animalis subsp. lactis Bl-04.
Ejby M, Fredslund F, Vujicic-Zagar A, Svensson B, Slotboom DJ, Abou Hachem M
Mol Microbiol 90 1100-12 (2013)
PMID: 24279727

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164255 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
XOS BINDING PROTEIN Chain: A
Molecule details ›
Chain: A
Length: 413 amino acids
Theoretical weight: 44.33 KDa
Source organism: Bifidobacterium animalis subsp. lactis Bl-04
Expression system: Escherichia coli BL21(DE3)
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

Carbohydrate polymer : NEW Components: XYP
Carbohydrate polymer
1 bound ligand:
Ligand P33 1 x P33
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21212
Unit cell:
a: 68.045Å b: 124.049Å c: 61.334Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.201 0.244
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Microbiota and Cancer: The Emerging Beneficial Role of Bifidobacteria in Cancer Immunotherapy.
Longhi et al. (2020)
9 more

1 mention without citation

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