5YWI

Crystal structure of Arabidopsis thaliana HPPD Truncated mutant complexed with NTBC

• PDB DOI: https://doi.org/10.2210/pdb5YWI/pdb

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


• Deposited: 2017-11-29 Released: 2019-01-16 
• Deposition Author(s): Yang, W.C., Chen, J.N.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.287 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 

Literature

Crystal structure of Arabidopsis thaliana HPPD Truncated mutant complexed with NTBC

Yang, W.C., Chen, J.N.

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: 46.07 kDa 
• Atom Count: 2,679 
• Modelled Residue Count: 362 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A	414	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NTD	C [auth A]	2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE C14 H10 F3 N O5 PMHVFNYNPNKNRO-UHFFFAOYSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 0.287 
• R-Value Work: 0.254 
• R-Value Observed: 0.255 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.601	α = 90
b = 83.568	β = 102.22
c = 64.15	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: 2019-01-16 
Deposition Author(s): Yang, W.C., Chen, J.N.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	21672079
National Science Foundation (China)	China	21332004

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description