8JJN

Structure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstroms resolution

• PDB DOI: https://doi.org/10.2210/pdb8JJN/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): Huang, W., Long, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.220 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Structure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstroms resolution

Huang, W., Long, F.

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: 107.09 kDa 
• Atom Count: 7,762 
• Modelled Residue Count: 960 
• Deposited Residue Count: 984 
• 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]	328	Variovorax paradoxus	Mutation(s): 0  Gene Names: JF629_18585
UniProt
Find proteins for A0A952K6X5 (Variovorax paradoxus) Explore A0A952K6X5  Go to UniProtKB:  A0A952K6X5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG (Subject of Investigation/LOI)	D [auth C], F [auth A], H [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
PO4 (Subject of Investigation/LOI)	E [auth C], G [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.220 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.825	α = 90
b = 55.792	β = 90.94
c = 108.076	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
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): Huang, W., Long, F.

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

Revision History  

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