Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 91.95 kDa 
• Atom Count: 6,723 
• Modelled Residue Count: 744 
• Deposited Residue Count: 792 
• Unique protein chains: 1

 5OYC

GH5 endo-xyloglucanase from Cellvibrio japonicus

• PDB DOI:  https://doi.org/10.2210/pdb5OYC/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio japonicus Ueda107
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-08 Released: 2018-02-07 
• Deposition Author(s): Attia, M., Nelson, C.E., Offen, W.A., Jain, N., Gardner, J.G., Davies, G.J., Brumer, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.137 
• R-Value Observed: 0.140 

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

• PubMed: 29467823 
• DOI: https://doi.org/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. 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellulase, putative, cel5D	A, B	396	Cellvibrio japonicus Ueda107	Mutation(s): 0  Gene Names: cel5D, CJA_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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	EA [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
PG4	DA [auth B], O [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	AA [auth B], BA [auth B], CA [auth B], N [auth A], Z [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.204 
• R-Value Work: 0.137 
• R-Value Observed: 0.140 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.004	α = 90
b = 96.434	β = 90
c = 158.954	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Attia, M., Nelson, C.E., Offen, W.A., Jain, N., Gardner, J.G., Davies, G.J., Brumer, H.

Revision History  

• 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