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Yorodumi- EMDB-28283: Subtomogram average of T4SS of Coxiella burnetii at pH7 with an i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28283 | |||||||||
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Title | Subtomogram average of T4SS of Coxiella burnetii at pH7 with an inner membrane mask | |||||||||
Map data | T4SS of Coxiella burnetii at pH 7 with an inner membrane mask only | |||||||||
Sample |
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Keywords | Bacterial secretion system / MEMBRANE PROTEIN | |||||||||
Biological species | Coxiella burnetii (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 51.0 Å | |||||||||
Authors | Kaplan M / Shepherd DC / Vankadari N / Kim KW / Larson CL / Przemyslaw D / Beare PA / Krzymowski E / Heinzen RA / Jensen GJ / Ghosal D | |||||||||
Funding support | United States, Australia, 2 items
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Citation | Journal: To Be Published Title: Subtomogram average of T4SS of Coxiella burnetii at pH7 with an inner membrane mask Authors: Kaplan M / Shepherd DC / Vankadari N / Kim KW / Larson CL / Przemyslaw D / Beare PA / Krzymowski E / Heinzen RA / Jensen GJ / Ghosal D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28283.map.gz | 578.5 KB | EMDB map data format | |
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Header (meta data) | emd-28283-v30.xml emd-28283.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_28283.png | 53.4 KB | ||
Filedesc metadata | emd-28283.cif.gz | 3.8 KB | ||
Others | emd_28283_half_map_1.map.gz emd_28283_half_map_2.map.gz | 559 KB 895.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28283 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28283 | HTTPS FTP |
-Validation report
Summary document | emd_28283_validation.pdf.gz | 565.8 KB | Display | EMDB validaton report |
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Full document | emd_28283_full_validation.pdf.gz | 565.3 KB | Display | |
Data in XML | emd_28283_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | emd_28283_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28283 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28283 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_28283.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | T4SS of Coxiella burnetii at pH 7 with an inner membrane mask only | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 8.073 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Even half map
File | emd_28283_half_map_1.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Odd half map
File | emd_28283_half_map_2.map | ||||||||||||
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Annotation | Odd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T4SS of Coxiella burnetii at pH 7 with an inner membrane mask
Entire | Name: T4SS of Coxiella burnetii at pH 7 with an inner membrane mask |
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Components |
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-Supramolecule #1: T4SS of Coxiella burnetii at pH 7 with an inner membrane mask
Supramolecule | Name: T4SS of Coxiella burnetii at pH 7 with an inner membrane mask type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Coxiella burnetii (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.625 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C13 (13 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 51.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 726 |
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Extraction | Number tomograms: 88 / Number images used: 726 |
Final angle assignment | Type: NOT APPLICABLE |