5OYD

GH5 endo-xyloglucanase from Cellvibrio japonicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

In vitro and in vivo characterization of threeCellvibrio japonicusglycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions.

Attia, M.A.Nelson, C.E.Offen, W.A.Jain, N.Davies, G.J.Gardner, J.G.Brumer, H.

(2018) Biotechnol Biofuels 11: 45-45

  • DOI: 10.1186/s13068-018-1039-6
  • Primary Citation of Related Structures:  
    5OYC, 5OYD, 5OYE

  • PubMed Abstract: 
  • Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides ...

    Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo -xyloglucanases were unresolved.


    Organizational Affiliation

    6Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellulase, putative, cel5DA, B396Cellvibrio japonicus Ueda107Mutation(s): 0 
Gene Names: cel5DCJA_3010
EC: 3.2.1.151 (PDB Primary Data), 3.2.1.4 (UniProt)
UniProt
Find proteins for B3PD52 (Cellvibrio japonicus (strain Ueda107))
Explore B3PD52 
Go to UniProtKB:  B3PD52
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-N-acetyl-beta-D-glucopyranosylamineC6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81585VK
GlyCosmos:  G81585VK
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-N-acetyl-beta-D-glucopyranosylamineD7N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G18905CN
GlyCosmos:  G18905CN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.455α = 90
b = 97.598β = 90
c = 157.196γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary