8GKN | pdb_00008gkn

Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with S-naringenin

• PDB DOI: https://doi.org/10.2210/pdb8GKN/pdb

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


• Deposited: 2023-03-20 Released: 2023-09-13 
• Deposition Author(s): Arriaza, R.H., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.
• Funding Organization(s): National Institute of Food and Agriculture (NIFA, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with S-naringenin

Arriaza, R.H., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 99.25 kDa 
• Atom Count: 6,845 
• Modeled Residue Count: 854 
• Deposited Residue Count: 874 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 202A2	A, B	437	Tetranychus urticae	Mutation(s): 0  Gene Names: 107367435, UGT202A2
UniProt
Find proteins for T1KUK4 (Tetranychus urticae) Explore T1KUK4  Go to UniProtKB:  T1KUK4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth A], E [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
NAR (Subject of Investigation/LOI)	D [auth A], F [auth B]	NARINGENIN C15 H12 O5 FTVWIRXFELQLPI-ZDUSSCGKSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.728	α = 90
b = 167.566	β = 90
c = 63.108	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-3000	data reduction
MOLREP	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Arriaza, R.H., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.

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Funding Organization	Location	Grant Number
National Institute of Food and Agriculture (NIFA, United States)	United States	#2020-67014- 31179

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release