› 5m7i

X-ray diffraction
2.1Å resolution

Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannobiose

Released:
DOI: 10.2210/pdb5m7i/pdb
PDB entry 5m7i coloured by chain, front view.
PDB entry 5m7i coloured by chain, side view.
PDB entry 5m7i coloured by chain, top view.
Source organism: Clostridium perfringens str. 13
Primary publication:
Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 α-Mannosidases.
Alonso-Gil S, Males A, Fernandes PZ, Williams SJ, Davies GJ, Rovira C
J Am Chem Soc 139 1085-1088 (2017)
PMID: 28026180

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-186906 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Glycoside hydrolase family 125 protein Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 50.86 KDa
Source organism: Clostridium perfringens str. 13
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8XNB2 (Residues: 1-427; Coverage: 100%)
Gene name: CPE0426
Sequence domains: Metal-independent alpha-mannosidase (GH125)
Structure domains: Glycosyltransferase

Ligands and Environments

Carbohydrate polymer : NEW Components: BMA, MAN
Carbohydrate polymer
No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 61.296Å b: 43.734Å c: 85.407Å
α: 90° β: 96.87° γ: 90°
R-values:
R R work R free
0.195 0.192 0.247
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions.
Franconetti et al. (2021)
6 other articles

1 mention without citation

Unlocking the Hydrolytic Mechanism of GH92 α-1,2-Mannosidases: Computation Inspires the use of C-Glycosides as Michaelis Complex Mimics.
Alonso-Gil et al. (2022)