› 5j7z

X-ray diffraction
2.15Å resolution

Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM1

Released:
DOI: 10.2210/pdb5j7z/pdb
PDB entry 5j7z coloured by chain, front view.
PDB entry 5j7z coloured by chain, side view.
PDB entry 5j7z coloured by chain, top view.
Source organism: Rhodococcus hoagii 103S
Primary publication:
Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases.
Han YB, Chen LQ, Li Z, Tan YM, Feng Y, Yang GY
J Biol Chem 292 4789-4800 (2017)
PMID: 28179425

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-165857 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Putative secreted endoglycosylceramidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 500 amino acids
Theoretical weight: 53.87 KDa
Source organism: Rhodococcus hoagii 103S
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC, GAL, NGA, SIA
Carbohydrate polymer
2 bound ligands:
Ligand NA 2 x NA
Ligand 18C 1 x 18C
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 192.283Å b: 48.921Å c: 120.227Å
α: 90° β: 113.95° γ: 90°
R-values:
R R work R free
0.169 0.167 0.203
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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Citations

3 review citations

Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation.
Botha et al. (2018)
2 more

6 mentions without citation

The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes.
Liu et al. (2018)
5 more