9KGM | pdb_00009kgm

Complex structure of OsHPPD with MBQ

• PDB DOI: https://doi.org/10.2210/pdb9KGM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-08 Released: 2025-11-12 
• Deposition Author(s): Yang, G.-F., Lin, H.-Y., Dong, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.292 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

Complex structure of OsHPPD with MBQ

Yang, G.-F., Lin, H.-Y., Dong, J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 94.93 kDa 
• Atom Count: 5,571 
• Modeled Residue Count: 765 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A, B	446	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: OSJNBa0085K21.52, P0669G09.6
UniProt
Find proteins for Q6H4V1 (Oryza sativa subsp. japonica) Explore Q6H4V1  Go to UniProtKB:  Q6H4V1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
92X	D [auth A], F [auth B]	1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione C24 H22 N2 O5 ZGLNNDUJJLHJTE-UHFFFAOYSA-N
CO	C [auth A], E [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.292 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.676	α = 90
b = 153.676	β = 90
c = 81.588	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: 2025-11-12 
Deposition Author(s): Yang, G.-F., Lin, H.-Y., Dong, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release