› 8k2k

X-ray diffraction
1.75Å resolution

Crystal structure of Group 3 Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaDssm in complex with GalNAc-thiazoline

Released:
DOI: 10.2210/pdb8k2k/pdb
PDB entry 8k2k coloured by chain, front view.
PDB entry 8k2k coloured by chain, side view.
PDB entry 8k2k coloured by chain, top view.
Source organism: metagenome
Primary publication:
Genetic and functional diversity of β-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Sumida T, Hiraoka S, Usui K, Ishiwata A, Sengoku T, Stubbs KA, Tanaka K, Deguchi S, Fushinobu S, Nunoura T
OpenAccess logo Nat Commun 15 3543 (2024)
PMID: 38730244

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-243466 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Oligosaccharide/Monosaccharide-releasing beta-N-acetylgalactosaminidase Chain: A
Molecule details ›
Chain: A
Length: 542 amino acids
Theoretical weight: 62.26 KDa
Source organism: metagenome
Expression system: Escherichia coli

Ligands and Environments

4 bound ligands:
Ligand GNL 1 x GNL
Ligand GOL 1 x GOL
Ligand SO4 2 x SO4
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: P43212
Unit cell:
a: 53.537Å b: 53.537Å c: 428.292Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.177 0.176 0.206
Expression system: Escherichia coli

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