|Entry||Database: EMDB / ID: 1637|
|Title||Proteome organization in a genome-reduced bacterium -Topoisomerase of Mycoplasma pneumoniae -|
|Keywords||Topoisomerase / Mycoplasma pneumoniae / single particle|
|Sample||Topoisomerase from Mycoplasma pneumoniae|
|Source||Mycoplasma pneumoniae / bacteria / マイコプラズマ・ニューモニアエ, 肺炎マイコプラズマ|
|Map data||Map of topoisomerase|
|Method||single particle reconstruction, at 21.5 A resolution|
|Authors||Kuhner S / vanNoort V / Betts MJ / Leo-Macias A / Batisse C / Rode M / Yamada T / Maier T / Bader S / Beltran-Alvarez P / Castano-Diez D / Chen W-H / Devos D / Guell Cargol M / Norambuena T / Racke I / Rybin V / Schmidt A / Yus E / Aebersold R / Herrmann R / Bottcher B / Frangakis AS / Russell RB / Serrano L / Bork P / Gavin A-C|
|Citation||Science, 2009, 326, 1235-1240|
Science, 2009, 326, 1235-1240 StrPapers
|Date||Deposition: Aug 3, 2009 / Header (metadata) release: Jun 11, 2010 / Map release: Jun 11, 2010 / Last update: Aug 3, 2009|
Downloads & links
|File||emd_1637.map.gz (map file in CCP4 format, 1025 KB)|
|Projections & slices||Size of images: |
Images are generated by Spider package.
|Voxel size||X=Y=Z: 5.2 A|
CCP4 map header:
-Entire Topoisomerase from Mycoplasma pneumoniae
|Entire||Name: Topoisomerase from Mycoplasma pneumoniae / Details: Sample was fixed following the GRAFIX protocol / Number of components: 1|
-Component #1: protein, Topoisomerase
|Sample solution||Buffer solution: 50mM Hepes, 20% glycerol, 0.075% glutaraldehyde, 100mM NaCl, 1.5 mM MgCl2|
|Support film||400 mesh copper grid|
|Staining||Grids were prepared by sandwich negative stain the sample was adsorbed to carbon on mica and floated on 1 % uranyl acetate the carbon was picked up with an uncoated grid then a second piece of carbon, which was also floated on 1% uranyl acetate, was picked up with the same grid sandwiching the sample between the two layers of carbon|
|Vitrification||Instrument: NONE / Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM200FEG|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 27500 X (nominal)|
Astigmatism: Corrected at 200000 times magnification on graininess of carbon
Cs: 2 mm / Imaging mode: BRIGHT FIELD
|Specimen Holder||Holder: Eucentric / Model: SIDE ENTRY, EUCENTRIC|
|Camera||Detector: GENERIC CCD|
|Image acquisition||Number of digital images: 70 / Sampling size: 14.22 microns / Bit depth: 12|
Details: Images were recorded on CCD, no scanning sampling step size was adjusted to calibrated image size
|Processing||Method: single particle reconstruction / Number of projections: 4767 / Applied symmetry: C1 (asymmetric)|
|3D reconstruction||Algorithm: Projection matching / Software: IMAGIC, SPIDER, EMAN|
Details: Spider option BP 32F Back Projection - 3D, Sampled, Interpolated in Fourier space
Resolution: 21.5 A / Resolution method: FSC 0.5
-Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
-Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
+Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi