+Open data
-Basic information
Entry | Database: PDB / ID: 4boq | ||||||
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Title | Structure of OTUD2 OTU domain | ||||||
Components | UBIQUITIN THIOESTERASE OTU1 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of retrograde protein transport, ER to cytosol / protein K27-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity ...protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of retrograde protein transport, ER to cytosol / protein K27-linked deubiquitination / protein K11-linked deubiquitination / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / ERAD pathway / endoplasmic reticulum unfolded protein response / macroautophagy / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / ubiquitin protein ligase binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. ...Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 Title: Otu Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis. Authors: Mevissen, T.E.T. / Hospenthal, M.K. / Geurink, P.P. / Elliott, P.R. / Akutsu, M. / Arnaudo, N. / Ekkebus, R. / Kulathu, Y. / Wauer, T. / El Oualid, F. / Freund, S.M.V. / Ovaa, H. / Komander, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4boq.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4boq.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 4boq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/4boq ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4boq | HTTPS FTP |
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-Related structure data
Related structure data | 4bopC 4bosC 4bouC 4bozC 3by4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 20732.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 132-314 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: Q5VVQ6, ubiquitinyl hydrolase 1 | ||
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#2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % / Description: NONE |
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Crystal grow | Details: 0.8M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 0.1 M TRIS PH 7.5 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→33.32 Å / Num. obs: 30915 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 17.49 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.47→1.55 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BY4 Resolution: 1.47→28.727 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 18.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.266 Å2 / ksol: 0.405 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.47→28.727 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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