8OI3

Structure of NopD with AtSUMO2

• PDB DOI: https://doi.org/10.2210/pdb8OI3/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium, Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-03-22 Released: 2024-04-03 
• Deposition Author(s): Reverter, D., Li, Y.
• Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.204 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Structure of NopD with AtSUMO2

Reverter, D., Li, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.97 kDa 
• Atom Count: 4,523 
• Modelled Residue Count: 520 
• Deposited Residue Count: 598 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III effector	A, B	208	Bradyrhizobium	Mutation(s): 0  Gene Names: nopD
UniProt
Find proteins for A0A2U9K2V6 (Bradyrhizobium sp) Explore A0A2U9K2V6  Go to UniProtKB:  A0A2U9K2V6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Small ubiquitin-related modifier 2	C, D	91	Arabidopsis thaliana	Mutation(s): 0  Gene Names: SUMO2, SUM2, At5g55160, MCO15.11
UniProt
Find proteins for Q9FLP6 (Arabidopsis thaliana) Explore Q9FLP6  Go to UniProtKB:  Q9FLP6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AYE (Subject of Investigation/LOI)	E [auth A], F [auth B]	prop-2-en-1-amine C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.204 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.851	α = 90
b = 86.826	β = 90
c = 90.485	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Reverter, D., Li, Y.

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Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	--

Revision History  

• Version 1.0: 2024-04-03
  Type: Initial release