› 6epz

X-ray diffraction
1.8Å resolution

Structure of the periplasmic binding protein MelB (Atu4661) in complex with melibiose from Agrobacterium fabrum C58

Released:
DOI: 10.2210/pdb6epz/pdb
PDB entry 6epz coloured by chain, front view.
PDB entry 6epz coloured by chain, side view.
PDB entry 6epz coloured by chain, top view.
Source organism: Agrobacterium tumefaciens
Primary publication:
The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum.
Meyer T, Vigouroux A, Aumont-Nicaise M, Comte G, Vial L, Lavire C, Moréra S
J Biol Chem 293 7930-7941 (2018)
PMID: 29602905

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-242629 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Periplasmic alpha-galactoside-binding protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 683 amino acids
Theoretical weight: 76.36 KDa
Source organism: Agrobacterium tumefaciens
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A083ZM57 (Residues: 19-695; Coverage: 100%)
Sequence domains: Bacterial extracellular solute-binding proteins, family 5 Middle

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, GLA
Carbohydrate polymer
5 bound ligands:
Ligand MG 5 x MG
Ligand EDO 9 x EDO
Ligand NA 28 x NA
Ligand CL 1 x CL
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: C2
Unit cell:
a: 351.61Å b: 73.73Å c: 107.58Å
α: 90° β: 105.38° γ: 90°
R-values:
R R work R free
0.178 0.177 0.195
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Ecological Conditions and Molecular Determinants Involved in Agrobacterium Lifestyle in Tumors.
Meyer et al. (2019)
9 other articles

1 mention without citation

The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogen Agrobacterium fabrum.
Meyer et al. (2018)