› 2cdo

X-ray diffraction
1.64Å resolution

structure of agarase carbohydrate binding module in complex with neoagarohexaose

Released:
DOI: 10.2210/pdb2cdo/pdb
PDB entry 2cdo coloured by chain, front view.
PDB entry 2cdo coloured by chain, side view.
PDB entry 2cdo coloured by chain, top view.
Source organism: Saccharophagus degradans
Primary publication:
Family 6 carbohydrate binding modules in beta-agarases display exquisite selectivity for the non-reducing termini of agarose chains.
Henshaw J, Horne-Bitschy A, van Bueren AL, Money VA, Bolam DN, Czjzek M, Ekborg NA, Weiner RM, Hutcheson SW, Davies GJ, Boraston AB, Gilbert HJ
J Biol Chem 281 17099-17107 (2006)
PMID: 16601125

Function and Biology Details

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-179524 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Beta-agarase I Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 160 amino acids
Theoretical weight: 17.11 KDa
Source organism: Saccharophagus degradans
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6DN99 (Residues: 451-593; Coverage: 24%)
Gene name: agaB
Sequence domains: Carbohydrate binding module (family 6)
Structure domains: Galactose-binding domain-like

Ligands and Environments

Carbohydrate polymer : NEW Components: GAL, AAL
Carbohydrate polymer
3 bound ligands:
Ligand CA 8 x CA
Ligand CL 10 x CL
Ligand EDO 7 x EDO
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P212121
Unit cell:
a: 54.036Å b: 54.979Å c: 196.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.241
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

8 review citations

The biochemistry and structural biology of plant cell wall deconstruction.
Gilbert HJ. (2010)
7 more

6 mentions without citation

Metagenomics and the protein universe.
Godzik A. (2011)
5 more