9GB9

Crystal structure of Lotus japonicus CERK6 kinase domain D460N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Two residues reprogram immunity receptor kinases to signal in nitrogen-fixing symbiosis

Tsitsikli, M.Simonsen, B.W.Larsen, M.M.Andersen, C.G.Gysel, K.Lironi, D.Kronauer, C.Rubsam, H.Luu, T.B.Hansen, S.B.Kaya, G.Stougaard, J.Andersen, K.R.Radutoiu, S.

(2024) bioRxiv 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LysM type receptor kinase
A, B, C, D
297Lotus japonicusMutation(s): 1 
Gene Names: LYS6
UniProt
Find proteins for D3KTZ6 (Lotus japonicus)
Explore D3KTZ6 
Go to UniProtKB:  D3KTZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3KTZ6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
L [auth B],
T [auth C]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
H [auth B]
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.92α = 106.457
b = 59.99β = 97.306
c = 103.74γ = 106.638
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF18OC0052855

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release