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Yorodumi- EMDB-4911: Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 3.04 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4911 | |||||||||
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Title | Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 3.04 Angstrom resolution | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
Authors | Safarian S / Hahn A / Kuehlbrandt W / Michel H | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the E. coli cytochrome bd-I oxidase at 2.68 ? resolution Authors: Safarian S / Hahn A / Kuehlbrandt S / Michel S | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4911.map.gz | 7.6 MB | EMDB map data format | |
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Header (meta data) | emd-4911-v30.xml emd-4911.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4911_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_4911.png | 103.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4911 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4911 | HTTPS FTP |
-Validation report
Summary document | emd_4911_validation.pdf.gz | 242.3 KB | Display | EMDB validaton report |
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Full document | emd_4911_full_validation.pdf.gz | 241.4 KB | Display | |
Data in XML | emd_4911_validation.xml.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4911 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4911 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4911.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cytochrome bd-I oxidase from E. coli
Entire | Name: Cytochrome bd-I oxidase from E. coli |
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Components |
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-Supramolecule #1: Cytochrome bd-I oxidase from E. coli
Supramolecule | Name: Cytochrome bd-I oxidase from E. coli / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: C43 / Recombinant plasmid: pet17b_cydABX-StrepII |
Molecular weight | Theoretical: 107.7 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7 mg/mL | ||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 5463 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 120 / Target criteria: Cross-correlation coefficient |
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