+Open data
-Basic information
Entry | Database: PDB / ID: 7ztb | ||||||
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Title | Structure of the Salmonella tRNA pyrophosphokinase CapRel | ||||||
Components | RelA/SpoT family protein | ||||||
Keywords | TOXIN / toxin-antitoxin / small alarmone synthetase / tRNA pyrophosphokinase / CapRel / bacterial defence | ||||||
Function / homology | guanosine tetraphosphate metabolic process / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Nucleotidyltransferase superfamily / RelA/SpoT family protein Function and homology information | ||||||
Biological species | Salmonella phage SJ46 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 Å | ||||||
Authors | Garcia-Pino, A. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Nature / Year: 2022 Title: Direct activation of a bacterial innate immune system by a viral capsid protein. Authors: Zhang, T. / Tamman, H. / Coppieters 't Wallant, K. / Kurata, T. / LeRoux, M. / Srikant, S. / Brodiazhenko, T. / Cepauskas, A. / Talavera, A. / Martens, C. / Atkinson, G.C. / Hauryliuk, V. / ...Authors: Zhang, T. / Tamman, H. / Coppieters 't Wallant, K. / Kurata, T. / LeRoux, M. / Srikant, S. / Brodiazhenko, T. / Cepauskas, A. / Talavera, A. / Martens, C. / Atkinson, G.C. / Hauryliuk, V. / Garcia-Pino, A. / Laub, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ztb.cif.gz | 281.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ztb.ent.gz | 227.5 KB | Display | PDB format |
PDBx/mmJSON format | 7ztb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/7ztb ftp://data.pdbj.org/pub/pdb/validation_reports/zt/7ztb | HTTPS FTP |
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-Related structure data
Related structure data | 6s2tS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42841.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella phage SJ46 (virus) / Gene: J46_0058 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A1B0VBT5 #2: Chemical | ChemComp-CL / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 277.16 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: peg 20000, 20% |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.312→68.1 Å / Num. obs: 20877 / % possible obs: 91.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 59.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.312→2.61 Å / Rmerge(I) obs: 1.292 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1044 / CC1/2: 0.531 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S2T Resolution: 2.312→68.1 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.357
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Displacement parameters | Biso mean: 68.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.312→68.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.312→2.5 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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