› 8y1m

X-ray diffraction
1.8Å resolution

Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose.

Released:
DOI: 10.2210/pdb8y1m/pdb
PDB entry 8y1m coloured by chain, front view.
PDB entry 8y1m coloured by chain, side view.
PDB entry 8y1m coloured by chain, top view.
Source organism: Bacillus sp. TAR1
Primary publication:
Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Nakamura T, Takita T, Kuwata K, Mizutani K, Mikami B, Nakamura S, Yasukawa K
OpenAccess logo Sci Rep 14 7767 (2024)
PMID: 38565938

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139610 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Endo-1,4-beta-xylanase A Chains: A, B
Molecule details ›
Chains: A, B
Length: 360 amino acids
Theoretical weight: 42.03 KDa
Source organism: Bacillus sp. TAR1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07528 (Residues: 46-396; Coverage: 95%)
Gene names: BH2120, xynA
Sequence domains: Glycosyl hydrolase family 10

Ligands and Environments

Carbohydrate polymer : NEW Components: XYP
Carbohydrate polymer
5 bound ligands:
Ligand CA 9 x CA
Ligand ACT 4 x ACT
Ligand MPD 7 x MPD
Ligand TRS 3 x TRS
Ligand PEG 2 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P21
Unit cell:
a: 88.702Å b: 53.335Å c: 96.567Å
α: 90° β: 93.58° γ: 90°
R-values:
R R work R free
0.168 0.166 0.202
Expression system: Escherichia coli BL21(DE3)

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