5JFK | pdb_00005jfk

Crystal structure of a TDR receptor

• PDB DOI: https://doi.org/10.2210/pdb5JFK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2016-04-19 Released: 2017-03-29 
• Deposition Author(s): Li, Z., Xu, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structure of a TDR receptor

Li, Z., Xu, G.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 137.07 kDa 
• Atom Count: 9,211 
• Modeled Residue Count: 1,154 
• Deposited Residue Count: 1,226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor-like protein kinase TDR	A, B	613	Arabidopsis thaliana	Mutation(s): 0  Gene Names: TDR, PXY, At5g61480, MCI2.4 EC: 2.7.11.1
UniProt
Find proteins for Q9FII5 (Arabidopsis thaliana) Explore Q9FII5  Go to UniProtKB:  Q9FII5
Glycosylation
Glycosylation Sites: 5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.250 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.336	α = 90
b = 92.336	β = 90
c = 250.127	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Li, Z., Xu, G.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary