› 3im0

X-ray diffraction
1.66Å resolution

Crystal structure of Chlorella virus vAL-1 soaked in 200mM D-glucuronic acid, 10% PEG-3350, and 200mM glycine-NaOH (pH 10.0)

Released:
DOI: 10.2210/pdb3im0/pdb
Model geometry
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PDB entry 3im0 coloured by chain, front view.
PDB entry 3im0 coloured by chain, side view.
PDB entry 3im0 coloured by chain, top view.
Source organism: Paramecium bursaria Chlorella virus CVK2
Primary publication:
Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action.
Ogura K, Yamasaki M, Yamada T, Mikami B, Hashimoto W, Murata K
J Biol Chem 284 35572-9 (2009)
PMID: 19846561

Function and Biology Details

Reaction catalysed: 
Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190119 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Polysaccharide lyase 14 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 252 amino acids
Theoretical weight: 28.04 KDa
Source organism: Paramecium bursaria Chlorella virus CVK2
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9DTZ2 (Residues: 106-349; Coverage: 70%)
Gene name: vAL-1
Sequence domains: Polysaccharide lyase 14
Structure domains: Jelly Rolls

Ligands and Environments

1 bound ligand:
Ligand BDP 1 x BDP
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 40.402Å b: 71.121Å c: 100.705Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.161 0.216
Expression system: Escherichia coli BL21(DE3)

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Citations

10 review citations

Structural and mechanistic classification of uronic acid-containing polysaccharide lyases.
Garron et al. (2010)
9 more

3 mentions without citation

The Astounding World of Glycans from Giant Viruses.
Speciale et al. (2022)
2 more

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