[English] 日本語
Yorodumi- EMDB-1680: Macromolecular crystal data phased by negative staining electron ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1680 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Macromolecular crystal data phased by negative staining electron microscopy reconstructions | |||||||||
Map data | Macromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle | |||||||||
Sample |
| |||||||||
Keywords | Negative staining / electron microscopy / reconstructions / phasing | |||||||||
Biological species | Candida albicans (yeast) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.0 Å | |||||||||
Authors | Trapani S / Schoehn G / Navaza J / Abergel C | |||||||||
Citation | Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: Macromolecular crystal data phased by negative-stained electron-microscopy reconstructions. Authors: Stefano Trapani / Guy Schoehn / Jorge Navaza / Chantal Abergel / Abstract: The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing ...The combination of transmission electron microscopy with X-ray diffraction data is usually limited to relatively large particles. Here, the approach is continued one step further by utilizing negative staining, a technique that is of wider applicability than cryo-electron microscopy, to produce models of medium-size proteins suitable for molecular replacement. The technique was used to solve the crystal structure of the dodecameric type II dehydroquinase enzyme from Candida albicans (approximately 190 kDa) and that of the orthologous Streptomyces coelicolor protein. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1680.map.gz | 2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1680-v30.xml emd-1680.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd-1680.png | 278.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1680 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1680 | HTTPS FTP |
-Validation report
Summary document | emd_1680_validation.pdf.gz | 208.4 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1680_full_validation.pdf.gz | 207.6 KB | Display | |
Data in XML | emd_1680_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1680 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1680 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_1680.map.gz / Format: CCP4 / Size: 2.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Macromolecular crystal data phased by negative staining electron microscopy reconstructions as a proof of principle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
Entire | Name: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ) |
---|---|
Components |
|
-Supramolecule #1000: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ)
Supramolecule | Name: Type-II dehydroquinase (DHQ) from Candida albicans (CaDHQ) type: sample / ID: 1000 / Oligomeric state: Dodecamer / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 200 KDa |
-Macromolecule #1: CaDHQ
Macromolecule | Name: CaDHQ / type: protein_or_peptide / ID: 1 / Name.synonym: CaDHQ / Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Candida albicans (yeast) |
Molecular weight | Theoretical: 17 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
---|---|
Buffer | pH: 7.4 / Details: 20mM NaCl, 10mM Tris-HCL |
Staining | Type: NEGATIVE Details: Negative staining using 1% methylamine vanadate, CH3NH2VO3 |
Grid | Details: 400 mesk copper grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER / Details: Negative staining at room temperature |
-Electron microscopy
Microscope | JEOL 1200EXII |
---|---|
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Details | Low dose negative staining |
Date | Dec 12, 2006 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 8 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: JEOL |
-Image processing
CTF correction | Details: Each negative |
---|---|
Final reconstruction | Applied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider Details: 7200 particles included in the reconstruction (out of 12000). 432 symmetry imposed Number images used: 7200 |
Final two d classification | Number classes: 114 |