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Yorodumi- EMDB-55952: Phage 812 baseplate in the pre-contraction state - core and wedge... -
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Open data
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Basic information
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| Title | Phage 812 baseplate in the pre-contraction state - core and wedge module proteins | |||||||||
Map data | Phage 812 baseplate in the pre-contraction state - core and wedge module proteins; postprocessed map | |||||||||
Sample |
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Keywords | phage / baseplate / VIRUS | |||||||||
| Function / homology | Function and homology informationsymbiont-mediated cytolysis of host cell / phosphoric diester hydrolase activity / cysteine-type peptidase activity / lipid metabolic process / proteolysis Similarity search - Function | |||||||||
| Biological species | Staphylococcus phage 812K1/420 (virus) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Binovsky J / Plevka P | |||||||||
| Funding support | European Union, Czech Republic, 2 items
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Citation | Journal: To Be PublishedTitle: Conformational changes of baseplate regulating tail contraction of Staphylococcus phage 812 Authors: Binovsky J / Plevka P | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_55952.map.gz | 34.3 MB | EMDB map data format | |
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| Header (meta data) | emd-55952-v30.xml emd-55952.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_55952_fsc.xml | 18 KB | Display | FSC data file |
| Images | emd_55952.png | 68.4 KB | ||
| Masks | emd_55952_msk_1.map | 512 MB | Mask map | |
| Filedesc metadata | emd-55952.cif.gz | 8.9 KB | ||
| Others | emd_55952_half_map_1.map.gz emd_55952_half_map_2.map.gz | 410.8 MB 410.7 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-55952 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-55952 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9tidMC ![]() 9ticC ![]() 9tieC ![]() 9tifC ![]() 9tigC ![]() 9tihC ![]() 9tiiC ![]() 9tijC ![]() 9tikC ![]() 9tilC ![]() 9timC ![]() 9tinC ![]() 9tioC ![]() 9tipC ![]() 9tisC ![]() 9titC ![]() 9tiwC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_55952.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Phage 812 baseplate in the pre-contraction state - core and wedge module proteins; postprocessed map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_55952_msk_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: Phage 812 baseplate in the pre-contraction state -...
| File | emd_55952_half_map_1.map | ||||||||||||
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| Annotation | Phage 812 baseplate in the pre-contraction state - core and wedge module proteins; half map1 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Phage 812 baseplate in the pre-contraction state -...
| File | emd_55952_half_map_2.map | ||||||||||||
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| Annotation | Phage 812 baseplate in the pre-contraction state - core and wedge module proteins; half map2 | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Staphylococcus phage 812K1/420
+Supramolecule #1: Staphylococcus phage 812K1/420
+Macromolecule #1: ORF58
+Macromolecule #2: ORF57
+Macromolecule #3: ORF56
+Macromolecule #4: ORF60
+Macromolecule #5: ORF59
+Macromolecule #6: ORF61
+Macromolecule #7: ORF62
+Macromolecule #8: ORF63
+Macromolecule #9: ORF49
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 8 Component:
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| Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
| Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV | ||||||||||||
| Details | 10e9 PFU/ml |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 26731 / Average exposure time: 2.0 sec. / Average electron dose: 40.8 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: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 35.8 |
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| Output model | ![]() PDB-9tid: |
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About Yorodumi



Staphylococcus phage 812K1/420 (virus)
Keywords
Authors
Czech Republic, 2 items
Citation




































Z (Sec.)
Y (Row.)
X (Col.)












































FIELD EMISSION GUN


