› 6haa

X-ray diffraction
1.7Å resolution

Structure of a covalent complex of endo-Xyloglucanase from Cellvibrio japonicus after reacting with XXXG(2F)-beta-DNP

Released:
DOI: 10.2210/pdb6haa/pdb
PDB entry 6haa coloured by chain, front view.
PDB entry 6haa coloured by chain, side view.
PDB entry 6haa coloured by chain, top view.
Source organism: Cellvibrio japonicus Ueda107
Primary publication:
Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases.
Jain N, Attia MA, Offen WA, Davies GJ, Brumer H
Org Biomol Chem 16 8732-8741 (2018)
PMID: 30387796

Function and Biology Details

Reaction catalysed: 
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109886 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Glycoside hydrolase family 5 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 396 amino acids
Theoretical weight: 44.34 KDa
Source organism: Cellvibrio japonicus Ueda107
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B3PD52 (Residues: 96-468; Coverage: 80%)
Gene names: CJA_3010, cel5D
Sequence domains: Cellulase (glycosyl hydrolase family 5)

Ligands and Environments

Carbohydrate polymer : NEW Components: G2F, BGC, XYS
Carbohydrate polymer
Carbohydrate polymer : NEW Components: G2F, BGC, XYS
Carbohydrate polymer
5 bound ligands:
Ligand GOL 3 x GOL
Ligand SO4 2 x SO4
Ligand PGE 2 x PGE
Ligand MES 2 x MES
Ligand 1PE 1 x 1PE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 56.058Å b: 97.206Å c: 156.677Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.218 0.271
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

QM/MM Simulations of Enzymatic Hydrolysis of Cellulose: Probing the Viability of an Endocyclic Mechanism for an Inverting Cellulase.
Pereira et al. (2021)

1 mention without citation

A Multiplexing Activity-Based Protein-Profiling Platform for Dissection of a Native Bacterial Xyloglucan-Degrading System.
McGregor et al. (2023)