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Yorodumi- EMDB-50071: Cryo-EM structure of the icosahedral lumazine synthase from Vicia... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50071 | |||||||||
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Title | Cryo-EM structure of the icosahedral lumazine synthase from Vicia faba. | |||||||||
Map data | Sharpened map (from RELION Postprocess) | |||||||||
Sample |
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Keywords | icosahedral enzyme / TRANSFERASE | |||||||||
Function / homology | 6,7-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 species | Vicia faba (fava bean) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Chee M / Trapani S / Hoh F / Lai Kee Him J / Yvon M / Blanc S / Bron P | |||||||||
Funding support | France, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50071.map.gz | 117 MB | EMDB map data format | |
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Header (meta data) | emd-50071-v30.xml emd-50071.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50071_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_50071.png | 231.7 KB | ||
Masks | emd_50071_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-50071.cif.gz | 5.4 KB | ||
Others | emd_50071_additional_1.map.gz emd_50071_half_map_1.map.gz emd_50071_half_map_2.map.gz | 95 MB 95.8 MB 95.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50071 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50071 | HTTPS FTP |
-Related structure data
Related structure data | 9ez8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_50071.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map (from RELION Postprocess) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2625 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_50071_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened map
File | emd_50071_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_50071_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_50071_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Icosahedral 60-mer
Entire | Name: Icosahedral 60-mer |
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Components |
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-Supramolecule #1: Icosahedral 60-mer
Supramolecule | Name: Icosahedral 60-mer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Vicia faba (fava bean) |
Molecular weight | Theoretical: 1.45 MDa |
-Macromolecule #1: 6,7-dimethyl-8-ribityllumazine synthase
Macromolecule | Name: 6,7-dimethyl-8-ribityllumazine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 6,7-dimethyl-8-ribityllumazine synthase |
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Source (natural) | Organism: Vicia faba (fava bean) |
Molecular weight | Theoretical: 16.505764 KDa |
Sequence | String: AVRHLTGSVT RTQGLRFAVV VARFNEIITR PLLEGALGTF KNYSVQDEDI DVVWVPGCFE IGAVATRLGK SGKYHAIICI GAVIRGDTT HYDAVANSAA SGVLSAGLNS GVPCIFGVLT CEDMDQAINR AGGKSGNKGA EAALTAIEMA SLFEHHLQ UniProtKB: 6,7-dimethyl-8-ribityllumazine synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 7.34 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: other / Details: poly-Ala model manually built using Coot |
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Output model | PDB-9ez8: |