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Yorodumi- EMDB-6840: The first reconstruction of beta-galactosidase solved by cryoARM200 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6840 | |||||||||
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Title | The first reconstruction of beta-galactosidase solved by cryoARM200 | |||||||||
Map data | First structure of the beta-galactosidase solved by cryoARM | |||||||||
Sample |
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Function / homology | Function and homology information alkali metal ion binding / lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding / magnesium ion binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Kato T / Terahara N / Namba K | |||||||||
Citation | Journal: To Be Published Title: The first reconstruction of beta-galactosidase solved by cryoARM200 Authors: Kato T / Namba K | |||||||||
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_6840.map.gz | 49.3 MB | EMDB map data format | |
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Header (meta data) | emd-6840-v30.xml emd-6840.xml | 12.6 KB 12.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6840_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_6840_1.png emd_6840_2.png | 430.4 KB 75.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6840 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6840 | HTTPS FTP |
-Validation report
Summary document | emd_6840_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_6840_full_validation.pdf.gz | 77.8 KB | Display | |
Data in XML | emd_6840_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6840 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6840 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
EM raw data | EMPIAR-10204 (Title: The first reconstruction of beta-galactosidase solved by cryoARM200 Data size: 321.4 Data #1: Unaligned multi-frame micrographs of beta-galactosidase recorded by CRYO ARM 200 [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6840.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | First structure of the beta-galactosidase solved by cryoARM | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.885 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 : Escherichia coli beta-galactosidase bound to phenylethyl beta-D-t...
Entire | Name: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG) |
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Components |
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-Supramolecule #1: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-t...
Supramolecule | Name: Escherichia coli beta-galactosidase bound to phenylethyl beta-D-thiogalactopyranoside (PETG) type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 465 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | This sample was monodisperse by adding 10 mM EDTA. |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Temperature | Min: 100.4 K / Max: 100.4 K |
Details | JEM-Z200FSC |
Image recording | Film or detector model: GATAN K2 IS (4k x 4k) / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 2161 / Average exposure time: 10.0 sec. / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.167 µm / Calibrated defocus min: 0.248 µm / Calibrated magnification: 56497 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL / Cooling holder cryogen: NITROGEN |