5JFI | pdb_00005jfi

Crystal structure of a TDIF-TDR complex

• PDB DOI: https://doi.org/10.2210/pdb5JFI/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): Xu, G., Li, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.267 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of a TDIF-TDR complex

Xu, G., Li, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 139.63 kDa 
• Atom Count: 9,400 
• Modeled Residue Count: 1,178 
• Deposited Residue Count: 1,250 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor-like protein kinase TDR	A, C [auth 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CLE41	B [auth C], D	12	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q84W98 (Arabidopsis thaliana) Explore Q84W98  Go to UniProtKB:  Q84W98

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	B [auth C], D	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.267 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.445	α = 90
b = 92.445	β = 90
c = 252.615	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): Xu, G., Li, Z.

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: 2025-04-02
  Changes: Data collection, Database references, Structure summary