7XNT

Crystal structure of PfHPPD-Y13161 complex

• PDB DOI: https://doi.org/10.2210/pdb7XNT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas fluorescens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2022-04-29 Released: 2022-12-14 
• Deposition Author(s): 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: 1.82 Å
• R-Value Free: 0.271 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 

Literature

Structural insights of 4-Hydrophenylpyruvate dioxygenase inhibition by structurally diverse small molecules

Dong, J., Dong, J., Yu, X.H., Yan, Y.C., Nan, J.X., He, B., Ye, B.Q., Yang, W.C., Lin, H.Y., Yang, G.F.

(2022) Adv Agrochem 

• DOI: https://doi.org/10.1016/j.aac.2022.10.002

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 162.29 kDa 
• Atom Count: 10,832 
• Modelled Residue Count: 1,324 
• Deposited Residue Count: 1,428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A [auth G], B [auth A], C [auth B], D [auth C]	357	Pseudomonas fluorescens	Mutation(s): 3  Gene Names: ALQ17_04098, AO066_02200

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
94L (Subject of Investigation/LOI)	F [auth G], H [auth A], J [auth B], L [auth C]	3-(2,6-dimethylphenyl)-1-methyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione C24 H22 N2 O5 IFHRYUOSJUERAZ-UHFFFAOYSA-N
CO (Subject of Investigation/LOI)	E [auth G], G [auth A], I [auth B], K [auth C]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.271 
• R-Value Work: 0.238 
• R-Value Observed: 0.239 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.943	α = 66.13
b = 73.041	β = 79.56
c = 87.963	γ = 69.1

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): 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: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description