› 4xps

X-ray diffraction
2.1Å resolution

Crystal structure of the mutant D365A of Pedobacter saltans GH31 alpha-galactosidase complexed with p-nitrophenyl-alpha-galactopyranoside

Released:
DOI: 10.2210/pdb4xps/pdb
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Source organism: Pseudopedobacter saltans
Primary publication:
Structural and biochemical characterization of novel bacterial α-galactosidases belonging to glycoside hydrolase family 31.
Miyazaki T, Ishizaki Y, Ichikawa M, Nishikawa A, Tonozuka T
Biochem J 469 145-58 (2015)
PMID: 25942325

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-101313 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-galactosidase Chain: A
Molecule details ›
Chain: A
Length: 720 amino acids
Theoretical weight: 81.38 KDa
Source organism: Pseudopedobacter saltans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0F7R6D6 (Residues: 20-719; Coverage: 100%)
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand GLA 1 x GLA
Ligand NPO 1 x NPO
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P43212
Unit cell:
a: 111.954Å b: 111.954Å c: 113.991Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.197 0.249
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

α-Glucosidases and α-1,4-glucan lyases: structures, functions, and physiological actions.
Okuyama et al. (2016)
11 other articles

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