8Y9O

Crystal structure of AtKAI2 in complex with KK181N1

• PDB DOI: https://doi.org/10.2210/pdb8Y9O/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-07 Released: 2024-12-04 
• Deposition Author(s): Wang, J.W., Miyakawa, T., Asami, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology, Chinese Scholarship Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 

Starting Model: experimental

Literature

Crystal structure of AtKAI2 in complex with KK181N1

Wang, J.W., Miyakawa, T., Asami, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 92.28 kDa 
• Atom Count: 6,852 
• Modelled Residue Count: 794 
• Deposited Residue Count: 831 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable esterase KAI2	A, B, C	277	Arabidopsis thaliana	Mutation(s): 0  Gene Names: KAI2, D14L, HTL, At4g37470, F6G17.120
UniProt
Find proteins for Q9SZU7 (Arabidopsis thaliana) Explore Q9SZU7  Go to UniProtKB:  Q9SZU7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IB0 (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	(7-methyl-2,3-dihydroindol-1-yl)-(1,2,3-triazol-1-yl)methanone C12 H12 N4 O SKGYNFOODZJUGQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.275 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.314	α = 90
b = 64.042	β = 104.79
c = 114.958	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Wang, J.W., Miyakawa, T., Asami, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H05266
Japan Science and Technology	Japan	--
Chinese Scholarship Council	China	--

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release