8JUP | pdb_00008jup

Crystal structure of a receptor like kinase from rice

• PDB DOI: https://doi.org/10.2210/pdb8JUP/pdb

• Classification: TRANSFERASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-27 Released: 2024-01-24 
• Deposition Author(s): Ming, Z., Zhao, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

An Active State Formation Mechanism of Receptor Kinase in Plant

Ming, Z., Zhao, Q.

(2024) Plant Commun 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.71 kDa 
• Atom Count: 2,467 
• Modeled Residue Count: 288 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LRR receptor-like serine/threonine-protein kinase FLS2	A	327	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: FLS2, Os04g0618700, LOC_Os04g52780, OsJ_16186 EC: 2.7.11.1
UniProt
Find proteins for Q0JA29 (Oryza sativa subsp. japonica) Explore Q0JA29  Go to UniProtKB:  Q0JA29

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.14	α = 90
b = 71.14	β = 90
c = 167.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-24 
Deposition Author(s): Ming, Z., Zhao, Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32160064

Revision History  

• Version 1.0: 2024-01-24
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary