› 8k2l

X-ray diffraction
1.95Å resolution

Crystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaP2 from Paenibacillus sp. TS12, apo form

Released:
DOI: 10.2210/pdb8k2l/pdb
PDB entry 8k2l coloured by chain, front view.
PDB entry 8k2l coloured by chain, side view.
PDB entry 8k2l coloured by chain, top view.
Source organism: Paenibacillus sp. TS12
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
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-243467 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Monosaccharide-releasing beta-N-acetylgalactosaminidase Chain: A
Molecule details ›
Chain: A
Length: 581 amino acids
Theoretical weight: 66.51 KDa
Source organism: Paenibacillus sp. TS12
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand BR 1 x BR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32XU
Spacegroup: C2
Unit cell:
a: 119.116Å b: 60.375Å c: 100.285Å
α: 90° β: 120.08° γ: 90°
R-values:
R R work R free
0.15 0.148 0.195
Expression system: Escherichia coli

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