8JJT

Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb8JJT/pdb

• Classification: TRANSFERASE
• Organism(s): Variovorax paradoxus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-31 Released: 2024-02-07 
• Deposition Author(s): Wei, H., Feng, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 

Starting Model: in silico

Literature

Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution

Wei, H., Feng, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.8 kDa 
• Atom Count: 8,150 
• Modelled Residue Count: 963 
• Deposited Residue Count: 993 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TIGR04348 family glycosyltransferase	A [auth C], B [auth A], C [auth B]	331	Variovorax paradoxus	Mutation(s): 0  Gene Names: JF629_18585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1 (Subject of Investigation/LOI)	D [auth C], E [auth A], F [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.215 
• R-Value Work: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.223	α = 90
b = 56.375	β = 91.106
c = 108.445	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Wei, H., Feng, L.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release