7DVG | pdb_00007dvg

Crystal structure of rice immune receptor RGA5-HMA5 mutant.

• PDB DOI: https://doi.org/10.2210/pdb7DVG/pdb

• Classification: PLANT PROTEIN
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-01-13 Released: 2022-01-19 
• Deposition Author(s): Zhang, X., Liu, J.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of rice immune receptor RGA5-HMA5.

Zhang, X., Liu, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.81 kDa 
• Atom Count: 1,098 
• Modeled Residue Count: 146 
• Deposited Residue Count: 146 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disease resistance protein RGA5	A, B	73	Oryza sativa Japonica Group	Mutation(s): 4  Gene Names: RGA5
UniProt
Find proteins for F7J0N2 (Oryza sativa subsp. japonica) Explore F7J0N2  Go to UniProtKB:  F7J0N2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.995	α = 90
b = 65.995	β = 90
c = 132.142	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-01-19 
Deposition Author(s): Zhang, X., Liu, J.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32030089

Revision History  

• Version 1.0: 2022-01-19
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description