› 2ddx

X-ray diffraction
0.86Å resolution

Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4

Released:
DOI: 10.2210/pdb2ddx/pdb
PDB entry 2ddx coloured by chain, front view.
PDB entry 2ddx coloured by chain, side view.
PDB entry 2ddx coloured by chain, top view.
Source organism: Vibrio sp. AX-4
Entry author: Sakaguchi K

Function and Biology Details

Reaction catalysed: 
Random hydrolysis of (1->3)-beta-D-glycosidic linkages in (1->3)-beta-D-xylans
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112715 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-1,3-xylanase XYL4 Chain: A
Molecule details ›
Chain: A
Length: 333 amino acids
Theoretical weight: 36.94 KDa
Source organism: Vibrio sp. AX-4
Expression system: Escherichia coli
UniProt:
  • Canonical: D5MP61 (Residues: 23-349; Coverage: 59%)
Gene name: xyl4
Structure domains: Glycosidases

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A, PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 51.873Å b: 75.654Å c: 82.119Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.14 0.139 0.148
Expression system: Escherichia coli

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