+
Open data
-
Basic information
Entry | Database: PDB / ID: 7jtu | ||||||
---|---|---|---|---|---|---|---|
Title | Cytidine deaminase T6S toxin from Pseudomonas syringae | ||||||
![]() |
| ||||||
![]() | TOXIN / Immunity / Type VI / T6SS / deaminase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bosch, D.E. / Hsu, F. / de Moraes, M.H. / Mougous, J.D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations. Authors: de Moraes, M.H. / Hsu, F. / Huang, D. / Bosch, D.E. / Zeng, J. / Radey, M.C. / Simon, N. / Ledvina, H.E. / Frick, J.P. / Wiggins, P.A. / Peterson, S.B. / Mougous, J.D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 61.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 435.9 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18559.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 22058.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Hanging drop diffusion. SsdA/SsdAI complex at 10 mg/mL was mixed 1:1 with crystallization solutions containing 20% PEG 3350, 0.1 M Bis-Tris:HCl pH 7.5 and 200 mM MgCl2. Cryopreservation was ...Details: Hanging drop diffusion. SsdA/SsdAI complex at 10 mg/mL was mixed 1:1 with crystallization solutions containing 20% PEG 3350, 0.1 M Bis-Tris:HCl pH 7.5 and 200 mM MgCl2. Cryopreservation was in crystallization solution with 20% glycerol. Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→35 Å / Num. obs: 17597 / % possible obs: 100 % / Redundancy: 28.6 % / Biso Wilson estimate: 79.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 3→3.03 Å / Redundancy: 29.6 % / Num. unique obs: 434 / Rpim(I) all: 0.279 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.64 Å2 / Biso mean: 79.8133 Å2 / Biso min: 42.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→33.39 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
|