+Open data
-Basic information
Entry | Database: PDB / ID: 5yet | ||||||
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Title | Structure of R354_WT | ||||||
Components | Uncharacterized protein R354 | ||||||
Keywords | NUCLEAR PROTEIN / MIMIVIRE / Cas4-like / nuclease / R354 | ||||||
Function / homology | Putative phage-type endonuclease / YqaJ viral recombinase / YqaJ-like viral recombinase domain / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like / Uncharacterized protein R354 Function and homology information | ||||||
Biological species | Acanthamoeba polyphaga mimivirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.806 Å | ||||||
Authors | Dou, C. / Yu, M.J. / Gu, Y.J. / Cheng, W. | ||||||
Citation | Journal: Iscience / Year: 2018 Title: Structural and Mechanistic Analyses Reveal a Unique Cas4-like Protein in the Mimivirus Virophage Resistance Element System. Authors: Dou, C. / Yu, M. / Gu, Y. / Wang, J. / Yin, K. / Nie, C. / Zhu, X. / Qi, S. / Wei, Y. / Cheng, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yet.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yet.ent.gz | 137.3 KB | Display | PDB format |
PDBx/mmJSON format | 5yet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/5yet ftp://data.pdbj.org/pub/pdb/validation_reports/ye/5yet | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47234.547 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 139-537 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acanthamoeba polyphaga mimivirus / Gene: MIMI_R354 / Production host: Escherichia coli DH1 (bacteria) / Strain (production host): DH1 / References: UniProt: Q5UQV1 #2: Water | ChemComp-HOH / | |
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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: 2.86 Å3/Da / Density % sol: 56.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 200mM ammonium tartrate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.806→48.949 Å / Num. obs: 22531 / % possible obs: 85.48 % / Redundancy: 4.8 % / Net I/σ(I): 13.05 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.806→48.949 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.806→48.949 Å
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Refine LS restraints |
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LS refinement shell |
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