8HX4

Crystal structure of AtHPPD-Y18549 complex

• PDB DOI: https://doi.org/10.2210/pdb8HX4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2023-01-03 Released: 2023-12-20 
• Deposition Author(s): Dong, J., Lin, H.-Y., Yang, G.-F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Literature

Crystal structure of AtHPPD-Y18549 complex

Dong, J., Lin, H.-Y., Yang, G.-F.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 46.57 kDa 
• Atom Count: 3,196 
• Modelled Residue Count: 382 
• Deposited Residue Count: 417 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	417	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
NQX	C [auth A]	6-[(R)-[(2R,6R)-2,6-bis(oxidanyl)cyclohexyl]-oxidanyl-methyl]-3-(4,6-dimethylpyrimidin-2-yl)-1,5-dimethyl-quinazoline-2,4-dione C23 H28 N4 O5 MLZUNIVRBBBYRG-HLIPFELVSA-N
MPD	D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.208 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.645	α = 90
b = 83.528	β = 100.32
c = 62.002	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-20 
Deposition Author(s): Dong, J., Lin, H.-Y., Yang, G.-F.

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

Revision History  

• Version 1.0: 2023-12-20
  Type: Initial release