› 6qe8

X-ray diffraction
1.79Å resolution

Crystal structure of Aspergillus niger GH11 endoxylanase XynA in complex with xylobiose epoxide activity based probe

Released:
DOI: 10.2210/pdb6qe8/pdb
PDB entry 6qe8 coloured by chain, front view.
PDB entry 6qe8 coloured by chain, side view.
PDB entry 6qe8 coloured by chain, top view.
Source organism: Aspergillus niger
Primary publication:
Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes.
Schröder SP, de Boer C, McGregor NGS, Rowland RJ, Moroz O, Blagova E, Reijngoud J, Arentshorst M, Osborn D, Morant MD, Abbate E, Stringer MA, Krogh KBRM, Raich L, Rovira C, Berrin JG, van Wezel GP, Ram AFJ, Florea BI, van der Marel GA, Codée JDC, Wilson KS, Wu L, Davies GJ, Overkleeft HS
ACS Cent Sci 5 1067-1078 (2019)
PMID: 31263766

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-157296 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endo-1,4-beta-xylanase A Chain: A
Molecule details ›
Chain: A
Length: 211 amino acids
Theoretical weight: 22.63 KDa
Source organism: Aspergillus niger
UniProt:
  • Canonical: P55329 (Residues: 1-211; Coverage: 100%)
Gene name: xynA
Sequence domains: Glycosyl hydrolases family 11

Ligands and Environments

3 bound ligands:
Ligand MES 1 x MES
Ligand SO4 8 x SO4
Ligand HZB 1 x HZB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P6522
Unit cell:
a: 67.508Å b: 67.508Å c: 165.752Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.177 0.223

Quick links

Citations

2 review citations

Recent advances in activity-based probes (ABPs) and affinity-based probes (AfBPs) for profiling of enzymes.
Fang et al. (2021)
1 more

2 mentions without citation

Dynamic and Functional Profiling of Xylan-Degrading Enzymes in Aspergillus Secretomes Using Activity-Based Probes.
Schröder et al. (2019)
1 more