8ZJB

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.311
R-Value Work: 0.256
R-Value Observed: 0.259

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

Organizational Affiliation

Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nudix hydrolase domain-containing protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G4Z7E8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free: 0.311
R-Value Work: 0.256
R-Value Observed: 0.259
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-03

Deposition Author(s):

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

Revision History (Full details and data files)

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

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.