7CTX | pdb_00007ctx

Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain(residues 388-401 deleted) in complex with AMP-PNP and magnesium

PDB DOI: https://doi.org/10.2210/pdb7CTX/pdb

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.243 (Depositor), 0.250 (DCC)
R-Value Work:
0.225 (Depositor), 0.227 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Arabidopsis thaliana SOBIR1 kinase domain(residues 388-401 deleted) in complex with AMP-PNP and magnesium

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

To be published.

Macromolecule Content

Total Structure Weight: 73.61 kDa
Atom Count: 4,598
Modeled Residue Count: 594
Deposited Residue Count: 646
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1	A, B	323	Arabidopsis thaliana	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9SKB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.243 (Depositor), 0.250 (DCC)
R-Value Work: 0.225 (Depositor), 0.227 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.389	α = 90
b = 50.732	β = 106.65
c = 93.066	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-27

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.