8BQA

CjCel5B endo-glucanase bound to CB665 covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8BQA/pdb

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


• Deposited: 2022-11-20 Released: 2023-11-29 
• Deposition Author(s): McGregor, N.G.S., de Boer, C., Overkleeft, H.S., Davies, G.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.226 
• R-Value Work: 0.186 

Literature

Dissection of a Native Bacterial Xyloglucan-degrading System using Activity-Based Probes

McGregor, N.G.S., de Boer, C., Foucart, Q., Beenakker, T., Willems, L., Overkleeft, H.S., Davies, G.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.26 kDa 
• Atom Count: 2,526 
• Modelled Residue Count: 298 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoglucanase	A [auth AAA]	306	Cellvibrio japonicus	Mutation(s): 0  Gene Names: cel5B, CJA_2983 EC: 3.2.1.4
UniProt
Find proteins for B3PCS3 (Cellvibrio japonicus (strain Ueda107)) Explore B3PCS3  Go to UniProtKB:  B3PCS3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RBH (Subject of Investigation/LOI)	B [auth AAA]	~{N}-[(2~{S},3~{S},4~{S},5~{R})-2-(hydroxymethyl)-4,5,6-tris(oxidanyl)oxan-3-yl]-2-oxidanyl-ethanamide C14 H27 N4 O9 RPRHCZBAXXPRCX-RGCYKPLRSA-O
YLL (Subject of Investigation/LOI)	D [auth AAA]	(1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL C7 H14 O6 QFYQIWDMMSKNFF-NYLBLOMBSA-N
XYS (Subject of Investigation/LOI)	C [auth AAA]	alpha-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-LECHCGJUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.226 
• R-Value Work: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.49	α = 90
b = 51.83	β = 110.427
c = 64.56	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): McGregor, N.G.S., de Boer, C., Overkleeft, H.S., Davies, G.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R001162/1
European Research Council (ERC)	European Union	2020-SyG-951231

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 2.0: 2024-01-24
  Changes: Advisory, Atomic model, Data collection, Derived calculations