› 5gkd

X-ray diffraction
2.19Å resolution

Structure of PL6 family alginate lyase AlyGC

Released:
DOI: 10.2210/pdb5gkd/pdb
PDB entry 5gkd coloured by chain, front view.
PDB entry 5gkd coloured by chain, side view.
PDB entry 5gkd coloured by chain, top view.
Source organism: Paraglaciecola chathamensis
Primary publication:
Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6.
Xu F, Dong F, Wang P, Cao HY, Li CY, Li PY, Pang XH, Zhang YZ, Chen XL
J Biol Chem 292 4457-4468 (2017)
PMID: 28154171

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
homo dimer
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-103696 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
AlyGC Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 726 amino acids
Theoretical weight: 80.38 KDa
Source organism: Paraglaciecola chathamensis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A1S4NYD7 (Residues: 1-726; Coverage: 100%)
Sequence domains: Chondroitinase B

Ligands and Environments

4 bound ligands:
Ligand CA 4 x CA
Ligand GOL 16 x GOL
Ligand PO4 12 x PO4
Ligand CO3 4 x CO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 116.608Å b: 142.84Å c: 126.276Å
α: 90° β: 111.09° γ: 90°
R-values:
R R work R free
0.167 0.165 0.197
Expression system: Escherichia coli BL21(DE3)

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Citations

3 review citations

Prebiotics from Seaweeds: An Ocean of Opportunity?
Cherry et al. (2019)
2 more

12 mentions without citation

Diversity of Three-Dimensional Structures and Catalytic Mechanisms of Alginate Lyases.
Xu et al. (2018)
11 more