+Open data
-Basic information
Entry | Database: PDB / ID: 8p1p | |||||||||
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Title | USP28 in complex with AZ1 | |||||||||
Components | Ubiquitin carboxyl-terminal hydrolase 28 | |||||||||
Keywords | ONCOPROTEIN / USP28 / Ubiquitin / inhibitor / AZ1 | |||||||||
Function / homology | Function and homology information protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | |||||||||
Authors | Sauer, F. / Karal-Nair, R. / Kisker, C. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: To Be Published Title: USP28 in complex with AZ1 Authors: Sauer, F. / Karal-Nair, R. / Kisker, C. #3: Journal: Mol Cell / Year: 2019 Title: Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities. Authors: Sauer, F. / Klemm, T. / Kollampally, R.B. / Tessmer, I. / Nair, R.K. / Popov, N. / Kisker, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p1p.cif.gz | 379.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p1p.ent.gz | 309.1 KB | Display | PDB format |
PDBx/mmJSON format | 8p1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/8p1p ftp://data.pdbj.org/pub/pdb/validation_reports/p1/8p1p | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: givenMatrix: (-0.937249275528, -0.0630279006468, -0.342915848661), (-0.00591682508518, 0.986258661315, -0.165102526214), (0.348609791463, -0.152713249987, -0.924743140864)Vector: 12. ...NCS oper: (Code: given Matrix: (-0.937249275528, -0.0630279006468, -0.342915848661), Vector: |
-Components
#1: Protein | Mass: 57924.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-DMS / | #4: Chemical | Mass: 422.212 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16BrF4NO2 / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.09 Å3/Da / Density % sol: 69.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.5 M sodium malonate pH 6.0 0.1 M sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→48.35 Å / Num. obs: 34461 / % possible obs: 94.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 60.95 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.76→3.008 Å / Num. unique obs: 1723 / CC1/2: 0.393 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→48.35 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3 / 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: 2.76→48.35 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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