+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16538 | |||||||||
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Title | Tomogram of Serratia marcescens in the post-spanin state (1) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Virulence / Secretion / Tc toxin / Type 10 secretion system / TOXIN | |||||||||
Biological species | Serratia marcescens (bacteria) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Sitsel O / Wang Z / Janning P / Kroczek L / Wagner T / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To Be Published Title: Specialized pathogenic cells release Tc toxins using a type 10 secretion system Authors: Sitsel O / Wang Z / Janning P / Kroczek L / Wagner T / Raunser S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16538.map.gz | 817.2 MB | EMDB map data format | |
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Header (meta data) | emd-16538-v30.xml emd-16538.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_16538.png | 272.9 KB | ||
Filedesc metadata | emd-16538.cif.gz | 4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16538 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16538 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16538.map.gz / Format: CCP4 / Size: 916.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.292 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Serratia marcescens strain BS 303, Ara-ChiR
Entire | Name: Serratia marcescens strain BS 303, Ara-ChiR |
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Components |
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-Supramolecule #1: Serratia marcescens strain BS 303, Ara-ChiR
Supramolecule | Name: Serratia marcescens strain BS 303, Ara-ChiR / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Serratia marcescens (bacteria) / Strain: BS 303, Ara-ChiR |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 6 / Details: Directly frozen in SOC growth media |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Aurion / Diameter: 5 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 42000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 95.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 39 |
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