8XT5 | pdb_00008xt5

The closed state of RGLG5-VWA

• PDB DOI: https://doi.org/10.2210/pdb8XT5/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-10 Released: 2025-01-22 
• Deposition Author(s): Wang, Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structure of the E3 ubiquitin ligase RGLG5 VWA domain

Wang, Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.07 kDa 
• Atom Count: 2,340 
• Modeled Residue Count: 272 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RGLG5	A	291	Arabidopsis thaliana	Mutation(s): 0  Gene Names: RGLG5, At1g67800 EC: 2.3.2.27
UniProt
Find proteins for Q8LB88 (Arabidopsis thaliana) Explore Q8LB88  Go to UniProtKB:  Q8LB88

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.998	α = 90
b = 66.945	β = 90
c = 84.884	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Wang, Q.

---

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

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release