6L8Z

Crystal structure of ugt transferase mutant in complex with UPG

• PDB DOI: https://doi.org/10.2210/pdb6L8Z/pdb

• Classification: TRANSFERASE
• Organism(s): Siraitia grosvenorii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-07 Released: 2020-04-01 
• Deposition Author(s): Li, J., Shan, N., Yang, J.G., Liu, W.D., Sun, Y.X.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.266 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Efficient O-Glycosylation of Triterpenes Enabled by Protein Engineering of Plant Glycosyltransferase UGT74AC1

Li, J., Yang, J.G., Mu, S., Shang, N., Liu, C., Zhu, Y., Cai, Y., Liu, P., Lin, J., Liu, W.D., Sun, Y.X., Ma, Y.

(2020) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b05232

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 51.9 kDa 
• Atom Count: 3,621 
• Modelled Residue Count: 444 
• Deposited Residue Count: 454 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A	454	Siraitia grosvenorii	Mutation(s): 0  Gene Names: UDPG1 EC: 2.4.1 (PDB Primary Data), 2.4.1.350 (UniProt)
UniProt
Find proteins for K7NBW3 (Siraitia grosvenorii) Explore K7NBW3  Go to UniProtKB:  K7NBW3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UPG (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE-GLUCOSE C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.266 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.311	α = 90
b = 69.153	β = 90
c = 141.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-04-01 
Deposition Author(s): Li, J., Shan, N., Yang, J.G., Liu, W.D., Sun, Y.X.

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

Revision History  

• Version 1.0: 2020-04-01
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary