7CTV | pdb_00007ctv

Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain D489A mutant in complex with AMP-PNP and magnesium

• PDB DOI: https://doi.org/10.2210/pdb7CTV/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-08-20 Released: 2022-04-27 
• Deposition Author(s): Wei, X., Wang, Y.L., Gu, T.Y., Xin, F.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain D489A mutant in complex with AMP-PNP and magnesium

Wei, X., Wang, Y.L., Gu, T.Y., Xin, F.J.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 76.63 kDa 
• Atom Count: 4,507 
• Modeled Residue Count: 592 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1	A, B	336	Arabidopsis thaliana	Mutation(s): 1  Gene Names: SOBIR1, EVR, At2g31880, F20M17.8 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9SKB2 (Arabidopsis thaliana) Explore Q9SKB2  Go to UniProtKB:  Q9SKB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.57	α = 90
b = 50.889	β = 95.348
c = 105.416	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Wei, X., Wang, Y.L., Gu, T.Y., Xin, F.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31571963

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description