8Y2L | pdb_00008y2l

The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile

• PDB DOI: https://doi.org/10.2210/pdb8Y2L/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-01-26 Released: 2025-01-29 
• Deposition Author(s): Fan, S., Wei, X., Lv, R., Wang, C., Tang, M., Jin, Y., Yang, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.95 Å
• R-Value Free: 
  0.300 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.241 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of Glucosyltransferase TcdB from Clostridioides difficile

Fan, S., Wei, X., Lv, R., Wang, C., Tang, M., Jin, Y., Yang, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 190.87 kDa 
• Atom Count: 13,343 
• Modeled Residue Count: 1,626 
• Deposited Residue Count: 1,638 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyltransferase TcdB	A, B, C	546	Clostridioides difficile	Mutation(s): 3  Gene Names: tcdB, toxB EC: 2.4.1 (PDB Primary Data), 3.4.22 (UniProt)
UniProt
Find proteins for P18177 (Clostridioides difficile) Explore P18177  Go to UniProtKB:  P18177

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MN (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.95 Å
• R-Value Free:  0.300 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.241 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.166	α = 90
b = 268.755	β = 90
c = 194.862	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Fan, S., Wei, X., Lv, R., Wang, C., Tang, M., Jin, Y., Yang, Z.

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Funding Organization	Location	Grant Number
Not funded		2018YFA0901800

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release