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- PDB-9ez8: Cryo-EM structure of the icosahedral lumazine synthase from Vicia... -

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Basic information

Entry
Database: PDB / ID: 9ez8
TitleCryo-EM structure of the icosahedral lumazine synthase from Vicia faba.
Components6,7-dimethyl-8-ribityllumazine synthaseLumazine synthase
KeywordsTRANSFERASE / icosahedral enzyme
Function / homology6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / Lumazine synthase / riboflavin synthase complex / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / riboflavin biosynthetic process / 6,7-dimethyl-8-ribityllumazine synthase
Function and homology information
Biological speciesVicia faba (fava bean)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsChee, M. / Trapani, S. / Hoh, F. / Lai Kee Him, J. / Yvon, M. / Blanc, S. / Bron, P.
Funding support France, 1items
OrganizationGrant numberCountry
Montpellier University of Excellence (MUSE)BLANC-MUSE2020-Multivir France
CitationJournal: To Be Published
Title: Cryo-EM structure of the icosahedral lumazine synthase from Vicia faba.
Authors: Chee, M. / Trapani, S. / Hoh, F. / Lai Kee Him, J. / Yvon, M. / Blanc, S. / Bron, P.
History
DepositionApr 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6,7-dimethyl-8-ribityllumazine synthase


Theoretical massNumber of molelcules
Total (without water)16,5061
Polymers16,5061
Non-polymers00
Water0
1
A: 6,7-dimethyl-8-ribityllumazine synthase
x 60


Theoretical massNumber of molelcules
Total (without water)990,34660
Polymers990,34660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein 6,7-dimethyl-8-ribityllumazine synthase / Lumazine synthase / DMRL synthase


Mass: 16505.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vicia faba (fava bean)
References: UniProt: A0A9D4WQC0, 6,7-dimethyl-8-ribityllumazine synthase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Icosahedral 60-mer / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 1.45 MDa / Experimental value: NO
Source (natural)Organism: Vicia faba (fava bean)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 7.34 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1.13CTF correction
9RELION4.0.0initial Euler assignment
10RELION4.0.0final Euler assignment
11RELION4.0.0classification
12RELION4.0.03D reconstruction
13Coot0.9.8.92model refinement
14PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64092 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingDetails: poly-Ala model manually built using Coot / Source name: Other / Type: other
RefinementCross valid method: NONE

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