+Open data
-Basic information
Entry | Database: PDB / ID: 5cht | ||||||
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Title | Crystal structure of USP18 | ||||||
Components | Ubl carboxyl-terminal hydrolase 18 | ||||||
Keywords | HYDROLASE / Ubiquitin-specific protease / ISG15 / interferon | ||||||
Function / homology | Function and homology information Regulation of IFNA/IFNB signaling / response to stilbenoid / Regulation of NF-kappa B signaling / ISG15 antiviral mechanism / TAK1-dependent IKK and NF-kappa-B activation / Ub-specific processing proteases / negative regulation of type I interferon-mediated signaling pathway / protein deubiquitination / antiviral innate immune response / response to bacterium ...Regulation of IFNA/IFNB signaling / response to stilbenoid / Regulation of NF-kappa B signaling / ISG15 antiviral mechanism / TAK1-dependent IKK and NF-kappa-B activation / Ub-specific processing proteases / negative regulation of type I interferon-mediated signaling pathway / protein deubiquitination / antiviral innate immune response / response to bacterium / ISG15-specific peptidase activity / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fritz, G. / Basters, A. | ||||||
Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Structural basis of the specificity of USP18 toward ISG15. Authors: Basters, A. / Geurink, P.P. / Rocker, A. / Witting, K.F. / Tadayon, R. / Hess, S. / Semrau, M.S. / Storici, P. / Ovaa, H. / Knobeloch, K.P. / Fritz, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cht.cif.gz | 259.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cht.ent.gz | 211.4 KB | Display | PDB format |
PDBx/mmJSON format | 5cht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cht_validation.pdf.gz | 438.2 KB | Display | wwPDB validaton report |
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Full document | 5cht_full_validation.pdf.gz | 448.2 KB | Display | |
Data in XML | 5cht_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5cht_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/5cht ftp://data.pdbj.org/pub/pdb/validation_reports/ch/5cht | HTTPS FTP |
-Related structure data
Related structure data | 5chvC 1nb8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37564.258 Da / Num. of mol.: 2 / Fragment: UNP residues 46-368 Source method: isolated from a genetically manipulated source Details: USP18 was truncated at the N-terminus. Residues 1-45 are missing. Residues 43, 44,45 given in the pdb are originating from the purification tag. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Usp18, Ubp43 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9WTV6, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.09 M succinate, pH 7.0, 13.5% (w/v) PEG 3350, 10 mM KBr |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→28 Å / Num. obs: 18487 / % possible obs: 99.76 % / Redundancy: 4.86 % / Rmerge(I) obs: 0.301 / Net I/σ(I): 6.29 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.96 % / Rmerge(I) obs: 2.771 / Mean I/σ(I) obs: 0.79 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NB8 Resolution: 2.8→27.772 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→27.772 Å
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Refine LS restraints |
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LS refinement shell |
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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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