› 4d6h

X-ray diffraction
1.65Å resolution

Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in complex with the type 1 blood group A-tetrasaccharide (E558A X02 mutant)

Released:
DOI: 10.2210/pdb4d6h/pdb
PDB entry 4d6h coloured by chain, front view.
PDB entry 4d6h coloured by chain, side view.
PDB entry 4d6h coloured by chain, top view.
Source organism: Streptococcus pneumoniae SP3-BS71
Primary publication:
Toward Efficient Enzymes for the Generation of Universal Blood through Structure-Guided Directed Evolution.
Kwan DH, Constantinescu I, Chapanian R, Higgins MA, Kötzler MP, Samain E, Boraston AB, Kizhakkedathu JN, Withers SG
J Am Chem Soc 137 5695-705 (2015)
PMID: 25870881

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-164378 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
GLYCOSIDE HYDROLASE Chain: A
Molecule details ›
Chain: A
Length: 599 amino acids
Theoretical weight: 69.04 KDa
Source organism: Streptococcus pneumoniae SP3-BS71
Expression system: Escherichia coli BL21(DE3)
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, GAL, FUC, A2G
Carbohydrate polymer
2 bound ligands:
Ligand EDO 2 x EDO
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-002
Spacegroup: C2221
Unit cell:
a: 92.26Å b: 154.75Å c: 97.16Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.145 0.186
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

What are the Limitations of Enzymes in Synthetic Organic Chemistry?
Reetz MT. (2016)
6 more

2 mentions without citation

Conformations of the type-1 lacto-N-biose I unit in protein complex structures.
Fushinobu S. (2018)
1 more