9J9K

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2F glucose

• PDB DOI: https://doi.org/10.2210/pdb9J9K/pdb
• Entry: 9J9K supersedes: 8J2T

• Classification: TRANSFERASE
• Organism(s): Nicotiana benthamiana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-08-22 Released: 2024-09-04 
• Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Glucosyl transferase NbUGT72AY1 co-crystallized with Scopoletin and UDP2F glucose

Arold, S.T., Hameed, U.F.S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 108.1 kDa 
• Atom Count: 7,493 
• Modelled Residue Count: 938 
• Deposited Residue Count: 950 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	475	Nicotiana benthamiana	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for A0A8K1ZRH3 (Nicotiana benthamiana) Explore A0A8K1ZRH3  Go to UniProtKB:  A0A8K1ZRH3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U2F (Subject of Investigation/LOI)	D [auth A], F [auth B]	URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE C15 H23 F N2 O16 P2 NGTCPFGWXMBZEP-NQQHDEILSA-N
T83 (Subject of Investigation/LOI)	C [auth A], E [auth B]	7-hydroxy-6-methoxy-2H-1-benzopyran-2-one C10 H8 O4 RODXRVNMMDRFIK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.607	α = 90
b = 114.919	β = 103.12
c = 104.249	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Arold, S.T., Hameed, U.F.S.
• This entry supersedes: 8J2T

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	King Abdullah University of Science and Technology

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release