[English] 日本語
![](img/lk-miru.gif)
- PDB-8ekm: Clostridioides difficile binary toxin translocase CDTb double mut... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8ekm | ||||||
---|---|---|---|---|---|---|---|
Title | Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A | ||||||
![]() | ADP-ribosyltransferase binding component | ||||||
![]() | TOXIN / translocase / binary toxin / calcium | ||||||
Function / homology | ![]() protein homooligomerization / transferase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å | ||||||
![]() | Abeyawardhane, D.L. / Pozharski, E. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Calcium-mediated Pore Formation of Clostridioides difficile Binary Toxin Authors: Abeyawardhane, D.L. / Adipietro, K.A. / Ruiz, R.G. / Varney, K.M. / Rustandi, R.R. / Silin, V.I. / Pozharski, E. / Weber, D.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 461.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 366.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 85.8 KB | Display | |
Data in CIF | ![]() | 125.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 28207MC ![]() 8ekkC ![]() 8eklC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 74591.078 Da / Num. of mol.: 7 / Mutation: D623A,D734A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||
Buffer component |
| |||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-
Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
---|---|
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-
Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 993305 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78587 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Accession code: 6UWR / Initial refinement model-ID: 1 / PDB-ID: 6UWR / Source name: PDB / Type: experimental model
| ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|