› 6ub3

X-ray diffraction
1.85Å resolution

Crystal structure of a GH128 (subgroup IV) endo-beta-1,3-glucanase from Lentinula edodes (LeGH128_IV) with laminaribiose at the surface-binding site

Released:
DOI: 10.2210/pdb6ub3/pdb
PDB entry 6ub3 coloured by chain, front view.
PDB entry 6ub3 coloured by chain, side view.
PDB entry 6ub3 coloured by chain, top view.
Source organism: Lentinula edodes
Primary publication:
Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family.
Santos CR, Costa PACR, Vieira PS, Gonzalez SET, Correa TLR, Lima EA, Mandelli F, Pirolla RAS, Domingues MN, Cabral L, Martins MP, Cordeiro RL, Junior AT, Souza BP, Prates ÉT, Gozzo FC, Persinoti GF, Skaf MS, Murakami MT
Nat Chem Biol 16 920-929 (2020)
PMID: 32451508

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124680 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Asl1-like glycosyl hydrolase catalytic domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 270 amino acids
Theoretical weight: 28.78 KDa
Source organism: Lentinula edodes
Expression system: Escherichia coli
UniProt:
  • Canonical: G9M5R4 (Residues: 21-267; Coverage: 100%)
Gene name: glu1
Sequence domains: Glycosyl hydrolase catalytic core

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC
Carbohydrate polymer
3 bound ligands:
Ligand CL 2 x CL
Ligand MES 1 x MES
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE W01B-MX2
Spacegroup: C2
Unit cell:
a: 157.024Å b: 46.693Å c: 115.252Å
α: 90° β: 119.7° γ: 90°
R-values:
R R work R free
0.176 0.174 0.209
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Discovery of new enzymatic functions and metabolic pathways using genomic enzymology web tools.
Zallot et al. (2021)
4 more