8ZI6 | pdb_00008zi6

Crystal structure of SrUGT76G4 in complex with UDP-glucose

• PDB DOI: https://doi.org/10.2210/pdb8ZI6/pdb

• Classification: TRANSFERASE
• Organism(s): Stevia rebaudiana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-13 Released: 2025-05-21 
• Deposition Author(s): Wang, Y., Li, T., Yin, H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.351 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Model: in silico

Literature

Functional Characterization and Structural Insights into SrUGT76G1-4 from Stevia Rebaudioside Reveal a Residue Critical for the Regioselectivity and efficient Rebaudioside M synthesis

Wang, Y., Li, T., Yin, H.

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 Evidence: gel filtration

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: 157.79 kDa 
• Atom Count: 9,426 
• Modeled Residue Count: 1,171 
• Deposited Residue Count: 1,374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UGT-glycosyltransferase 76G4	A, B, C	458	Stevia rebaudiana	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for Q6VAB4 (Stevia rebaudiana) Explore Q6VAB4  Go to UniProtKB:  Q6VAB4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG (Subject of Investigation/LOI)	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
PO4	G [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IPA	E [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.351 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.78	α = 90
b = 111.78	β = 90
c = 91.77	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Wang, Y., Li, T., Yin, H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release