[English] 日本語
Yorodumi- 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 | ||||||
Components | ADP-ribosyltransferase binding component | ||||||
Keywords | TOXIN / translocase / binary toxin / calcium | ||||||
Function / homology | Function and homology information protein homooligomerization / transferase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.56 Å | ||||||
Authors | Abeyawardhane, D.L. / Pozharski, E. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ekm.cif.gz | 461.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ekm.ent.gz | 366.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ekm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ekm_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8ekm_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8ekm_validation.xml.gz | 85.8 KB | Display | |
Data in CIF | 8ekm_validation.cif.gz | 125.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/8ekm ftp://data.pdbj.org/pub/pdb/validation_reports/ek/8ekm | HTTPS FTP |
-Related structure data
Related structure data | 28207MC 8ekkC 8eklC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-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.) Clostridioides difficile (bacteria) / Strain: R20291 / Gene: cdtB / Production host: Escherichia coli (E. coli) / References: UniProt: O32739 #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: Clostridioides difficile (bacteria) / Strain: R20291 | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
|