+Open data
-Basic information
Entry | Database: PDB / ID: 8cms | ||||||
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Title | OTUB2 in covalent complex with LN5P45 | ||||||
Components | Ubiquitin thioesterase OTUB2 | ||||||
Keywords | HYDROLASE / Chemical modification / ubiquitin / deubiquitinase / inhibitor | ||||||
Function / homology | Function and homology information negative regulation of double-strand break repair / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / proteolysis / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Gan, J. / de Vries, J. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2. Authors: Gan, J. / de Vries, J. / Akkermans, J.J.L.L. / Mohammed, Y. / Tjokrodirijo, R.T.N. / de Ru, A.H. / Kim, R.Q. / Vargas, D.A. / Pol, V. / Fasan, R. / van Veelen, P.A. / Neefjes, J. / van Dam, ...Authors: Gan, J. / de Vries, J. / Akkermans, J.J.L.L. / Mohammed, Y. / Tjokrodirijo, R.T.N. / de Ru, A.H. / Kim, R.Q. / Vargas, D.A. / Pol, V. / Fasan, R. / van Veelen, P.A. / Neefjes, J. / van Dam, H. / Ovaa, H. / Sapmaz, A. / Geurink, P.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cms.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cms.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cms_validation.pdf.gz | 680.9 KB | Display | wwPDB validaton report |
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Full document | 8cms_full_validation.pdf.gz | 682.6 KB | Display | |
Data in XML | 8cms_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 8cms_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/8cms ftp://data.pdbj.org/pub/pdb/validation_reports/cm/8cms | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 27405.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OTUB2, C14orf137, OTB2, OTU2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q96DC9, ubiquitinyl hydrolase 1 |
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#2: Chemical | ChemComp-V2X / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 %v/v 2-Propanol 13 %w/v PEG 4K 0.1 M HEPES pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→47.43 Å / Num. obs: 24095 / % possible obs: 99.6 % / Redundancy: 3.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.077 / Rrim(I) all: 0.142 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.295 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1360 / CC1/2: 0.338 / Rpim(I) all: 0.985 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→47.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.127 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.133 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→47.43 Å
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Refine LS restraints |
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LS refinement shell |
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