5FKS

Unraveling the first step of xyloglucan degradation by the soil saprophyte Cellvibrio japonicus through the functional and structural characterization of a potent GH74 endo-xyloglucanase

• PDB DOI: https://doi.org/10.2210/pdb5FKS/pdb

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


• Deposited: 2015-10-19 Released: 2015-11-25 
• Deposition Author(s): Attia, M., Stepper, J., Davies, G.J., Brumer, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.98 kDa 
• Atom Count: 6,183 
• Modelled Residue Count: 731 
• Deposited Residue Count: 731 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-GLUCANASE/XYLOGLUCANASE, PUTATIVE, GLY74A	A	731	Cellvibrio japonicus Ueda107	Mutation(s): 0  EC: 3.2.1 (PDB Primary Data), 3.2.1.151 (PDB Primary Data)
UniProt
Find proteins for B3PKK9 (Cellvibrio japonicus (strain Ueda107)) Explore B3PKK9  Go to UniProtKB:  B3PKK9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan:  G12985OQ GlyCosmos:  G12985OQ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	C	9		N/A
Glycosylation Resources
GlyTouCan:  G06184LI GlyCosmos:  G06184LI

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.213 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.36	α = 90
b = 127.69	β = 90
c = 73.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Attia, M., Stepper, J., Davies, G.J., Brumer, H.

Revision History  

• Version 1.0: 2015-11-25
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2016-05-18
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary