6SU6 | pdb_00006su6

Complex between a UDP-glucosyltransferase from Polygonum tinctorium capable of glucosylating indoxyl and UDP-glucose

• PDB DOI: https://doi.org/10.2210/pdb6SU6/pdb

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


• Deposited: 2019-09-13 Released: 2020-09-30 
• Deposition Author(s): Fredslund, F., Teze, D., Svensson, B., Adams, P.D., Welner, D.H.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering

Teze, D., Coines, J., Fredslund, F., Dubey, K.D., Bidart, G.N., Adams, P.D., Dueber, J.E., Svensson, B., Rovira, C., Welner, D.H.

(2021) ACS Catal 11

• DOI: https://doi.org/10.1021/acscatal.0c04171

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 110.18 kDa 
• Atom Count: 7,274 
• Modeled Residue Count: 922 
• Deposited Residue Count: 998 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	499	Persicaria tinctoria	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for A0A2R2JFJ4 (Persicaria tinctoria) Explore A0A2R2JFJ4  Go to UniProtKB:  A0A2R2JFJ4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.263 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.24	α = 90
b = 174.17	β = 90
c = 48.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Fredslund, F., Teze, D., Svensson, B., Adams, P.D., Welner, D.H.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17OC0025660
Novo Nordisk Foundation	Denmark	NNF10CC1016517

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2021-04-21
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description