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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free:
0.311 (Depositor), 0.305 (DCC)
R-Value Work:
0.256 (Depositor), 0.252 (DCC)
R-Value Observed:
0.259 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZJB

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 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
Modeled Residue Count: 1,241
Deposited Residue Count: 1,482
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.305 (DCC)
R-Value Work: 0.256 (Depositor), 0.252 (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

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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

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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.