+Open data
-Basic information
Entry | Database: PDB / ID: 7jtu | ||||||
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Title | Cytidine deaminase T6S toxin from Pseudomonas syringae | ||||||
Components |
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Keywords | TOXIN / Immunity / Type VI / T6SS / deaminase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas syringae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å | ||||||
Authors | Bosch, D.E. / Hsu, F. / de Moraes, M.H. / Mougous, J.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2021 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jtu.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jtu.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 7jtu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jtu_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 7jtu_full_validation.pdf.gz | 435.9 KB | Display | |
Data in XML | 7jtu_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 7jtu_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/7jtu ftp://data.pdbj.org/pub/pdb/validation_reports/jt/7jtu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18559.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Q0DAS4 |
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#2: Protein | Mass: 22058.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3M2XVH3 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.13 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.979 Å |
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 |
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Refinement | Method to determine structure: SAD / Resolution: 3→33.39 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.99 / Stereochemistry target values: MLHL
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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
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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