9QMT | pdb_00009qmt

Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Mesotrione (Mn)

• PDB DOI: https://doi.org/10.2210/pdb9QMT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-03-24 Released: 2026-04-08 
• Deposition Author(s): Alshref, F.M., Dhingra, S., Brewitz, L., Allen, M.D., Schofield, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC), Saudi Ministry of Education

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Arabidopsis thaliana 4-hydroxyphenylpyruvate dioxygenase in complex with Mesotrione (Mn)

Alshref, F.M., Dhingra, S., Brewitz, L., Allen, M.D., Schofield, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 45.86 kDa 
• Atom Count: 3,105 
• Modeled Residue Count: 376 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	412	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HPD, PDS1, At1g06570, F12K11.9 EC: 1.13.11.27
UniProt
Find proteins for P93836 (Arabidopsis thaliana) Explore P93836  Go to UniProtKB:  P93836

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
92L (Subject of Investigation/LOI)	C [auth A]	2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione C14 H13 N O7 S PILIZHLSOWYJPQ-UHFFFAOYSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.635	α = 90
b = 83.628	β = 100.64
c = 61.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-08 
Deposition Author(s): Alshref, F.M., Dhingra, S., Brewitz, L., Allen, M.D., Schofield, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V001892/1
Saudi Ministry of Education	Saudi Arabia	DM8000S4747

Revision History  

• Version 1.0: 2026-04-08
  Type: Initial release