+Open data
-Basic information
Entry | Database: PDB / ID: 6yk8 | ||||||
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Title | OTU-like deubiquitinase from Legionella -Lpg2529 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | CELL INVASION / deubiquitinase / legionella / OTU / effector protein | ||||||
Function / homology | : / Dot/Icm T4SS effector Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.42 Å | ||||||
Authors | Shin, D. / Dikic, I. | ||||||
Citation | Journal: Elife / Year: 2020 Title: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. Authors: Shin, D. / Bhattacharya, A. / Cheng, Y.L. / Alonso, M.C. / Mehdipour, A.R. / van der Heden van Noort, G.J. / Ovaa, H. / Hummer, G. / Dikic, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yk8.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yk8.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 6yk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yk8_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 6yk8_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 6yk8_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 6yk8_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/6yk8 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/6yk8 | 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: 34752.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2529 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSI8 #2: Chemical | ChemComp-PT / #3: 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: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25 % PEG3350, 100 mM Tris-HCl pH 8.5, 200 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.070333 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.070333 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→44.53 Å / Num. obs: 23185 / % possible obs: 99.23 % / Redundancy: 2 % / Biso Wilson estimate: 61.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03065 / Net I/σ(I): 14.85 |
Reflection shell | Resolution: 2.42→2.506 Å / Rmerge(I) obs: 0.3765 / Num. unique obs: 2278 / CC1/2: 0.811 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.42→44.53 Å / SU ML: 0.4094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9252
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→44.53 Å
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Refine LS restraints |
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LS refinement shell |
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