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)

Experimental Data Snapshot

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

Starting Model: other
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9D4WQC0
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Lai Kee Him, J.

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

Revision History (Full details and data files)

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

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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.