Database: EMDB / ID: 5438|
|Title||3D reconstruction of a self-assembling designed oligomer with octahedral symmetry|
|Keywords||octahedral symmetry / designed|
|Sample||Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L|
|Source||Salmonella enterica / bacteria|
|Map data||Reconstruction of designed self-assembling protein oligomer with octahedral symmetry|
|Method||single particle reconstruction, at 20 A resolution|
|Authors||Vollmar BS / King NP / Baker D / Gonen T|
|Citation||Science, 2012, 336, 1171-1174|
|Date||Deposition: Jun 24, 2012 / Header (metadata) release: Jun 29, 2012 / Map release: Jun 29, 2012 / Last update: Jun 24, 2012|
|3D viewer|| / |
Downloads & links
|File||emd_5438.map.gz (map file in CCP4 format, 6751 KB)|
|Projections & slices||Size of images: |
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.474 A|
CCP4 map header:
Entire Designed protein oligomer with octahedral symmetry. The model for...
|Entire||Name: Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L|
Details: Monodisperse sample / Number of components: 1 / Oligomeric State: 24
|Mass||Theoretical: 480 kDa|
Component #1: protein, Propanediol utilization polyhedral body protein PduT
|Protein||Name: Propanediol utilization polyhedral body protein PduT|
Details: Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Recombinant expression: Yes / Number of Copies: 24
|Source||Species: Salmonella enterica / bacteria|
|Source (engineered)||Expression System: Escherichia coli / bacteria / / Vector: pET29b|
|Sample solution||Specimen conc.: 0.3 mg/ml / Buffer solution: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT / pH: 8|
|Support film||Quantifoil R1.2/1.3 holey carbon 400 mesh copper grids|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %|
Method: Blotted with filter paper and plunged into liquid ethane.
Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI F20 / Date: Jul 12, 2011|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN|
|Lens||Magnification: 100000 X (nominal), 217096 X (calibrated) / Cs: 2.12 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: TVIPS TEMCAM-F816 (8k x 8k)|
|Image acquisition||Number of digital images: 565|
|Processing||Method: single particle reconstruction / Number of projections: 42025|
Details: Particles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).
Applied symmetry: O (octahedral)
|3D reconstruction||Software: FREALIGN / CTF correction: CTFFIND3|
Details: Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
Resolution: 20 A / Resolution method: FSC 0.5
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