› 2d22

X-ray diffraction
1.7Å resolution

Crystal structure of covalent glycosyl-enzyme intermediate of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

Released:
DOI: 10.2210/pdb2d22/pdb
PDB entry 2d22 coloured by chain, front view.
PDB entry 2d22 coloured by chain, side view.
PDB entry 2d22 coloured by chain, top view.
Source organism: Streptomyces olivaceoviridis
Primary publication:
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
Suzuki R, Fujimoto Z, Ito S, Kawahara S, Kaneko S, Taira K, Hasegawa T, Kuno A
J Biochem 146 61-70 (2009)
PMID: 19279191

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181928 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Beta-xylanase Chains: A, B
Molecule details ›
Chains: A, B
Length: 436 amino acids
Theoretical weight: 46.77 KDa
Source organism: Streptomyces olivaceoviridis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7SI98 (Residues: 1-436; Coverage: 100%)
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: XYS
Carbohydrate polymer
2 bound ligands:
Ligand SO4 5 x SO4
Ligand GOL 8 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P212121
Unit cell:
a: 78.691Å b: 93.956Å c: 139.721Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.186 0.207
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structure and function of carbohydrate-binding module families 13 and 42 of glycoside hydrolases, comprising a β-trefoil fold.
Fujimoto Z. (2013)
8 other articles

27 mentions without citation

The bright and the dark side of human antibody responses to flaviviruses: lessons for vaccine design.
Rey et al. (2018)
26 more