6IJ9

Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP

• PDB DOI: https://doi.org/10.2210/pdb6IJ9/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-09 Released: 2019-10-16 
• Deposition Author(s): Zong, G.N., Wang, X.Q.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.274 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Starting Model: experimental

Literature

Crystal Structure of Arabidopsis thaliana UGT89C1 complexed with UDP

Zong, G.N., Wang, X.Q.

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)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 194.33 kDa 
• Atom Count: 12,804 
• Modelled Residue Count: 1,619 
• Deposited Residue Count: 1,740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glycosyltransferase 89C1	A, B, C, D	435	Arabidopsis thaliana	Mutation(s): 0  EC: 2.4.1
UniProt
Find proteins for Q9LNE6 (Arabidopsis thaliana) Explore Q9LNE6  Go to UniProtKB:  Q9LNE6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	E [auth A], F [auth B], G [auth C], H [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.274 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.979	α = 90
b = 84.141	β = 108.9
c = 129.146	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-16 
Deposition Author(s): Zong, G.N., Wang, X.Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	2017YFA0504801

Revision History  

• Version 1.0: 2019-10-16
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary