9EZ8 | pdb_00009ez8

Cryo-EM structure of the icosahedral lumazine synthase from Vicia faba.

• PDB DOI: https://doi.org/10.2210/pdb9EZ8/pdb
• EM Map EMD-50071: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Vicia faba
• Mutation(s): No 


• Deposited: 2024-04-11 Released: 2024-05-22 
• Deposition Author(s): Chee, M., Trapani, S., Hoh, F., Lai Kee Him, J., Yvon, M., Blanc, S., Bron, P.
• Funding Organization(s): Montpellier University of Excellence (MUSE)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: other

Literature

Cryo-EM structure of the icosahedral lumazine synthase from Vicia faba.

Chee, M., Trapani, S., Hoh, F., Lai Kee Him, J., Yvon, M., Blanc, S., Bron, P.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 16.51 kDa 
• Atom Count: 1,158 
• Modeled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A	157	Vicia faba	Mutation(s): 0  EC: 2.5.1.78
UniProt
Find proteins for A0A9D4WQC0 (Pisum sativum) Explore A0A9D4WQC0  Go to UniProtKB:  A0A9D4WQC0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0.0
MODEL REFINEMENT	Coot	0.9.8.92
MODEL REFINEMENT	PHENIX	1.20.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Chee, M., Trapani, S., Hoh, F., Lai Kee Him, J., Yvon, M., Blanc, S., Bron, P.

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Funding Organization	Location	Grant Number
Montpellier University of Excellence (MUSE)	France	BLANC-MUSE2020-Multivir

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release