8ZJB | pdb_00008zjb

Oomycete Nudix effectors display WY-Nudix conformations with mRNA decapping activity

• PDB DOI: https://doi.org/10.2210/pdb8ZJB/pdb

• Classification: HYDROLASE
• Organism(s): Phytophthora sojae strain P6497
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-14 Released: 2024-07-03 
• Deposition Author(s): Xing, W., Xing, W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Literature

Oomycete Nudix effectors display WY-Nudix conformation and mRNA decapping activity.

Guo, B., Hu, Q., Wang, B., Yao, D., Wang, H., Kong, G., Han, C., Dong, S., Liu, F., Xing, W., Wang, Y.

(2024) J Integr Plant Biol 66: 1548-1552

• PubMed: 38888246 
• DOI: https://doi.org/10.1111/jipb.13712
• Primary Citation of Related Structures:  
  8ZJB

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Organizational Affiliation: 
• Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China.
Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, 75390, Texas, USA.
Institute of Aging & Tissue Regeneration, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
College of Agriculture, Guizhou University, Guiyang, 550025, China.
College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 163.14 kDa 
• Atom Count: 9,168 
• Modeled Residue Count: 1,241 
• Deposited Residue Count: 1,482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase domain-containing protein	A, B, C, D, E, F	247	Phytophthora sojae strain P6497	Mutation(s): 0  Gene Names: PHYSODRAFT_285308
UniProt
Find proteins for G4Z7E8 (Phytophthora sojae (strain P6497)) Explore G4Z7E8  Go to UniProtKB:  G4Z7E8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.19 Å
• R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.364	α = 90
b = 164.496	β = 90
c = 169.545	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
DIALS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Xing, W., Xing, W.

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

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release
  
• Version 1.1: 2024-08-28
  Changes: Database references