+Open data
-Basic information
Entry | Database: PDB / ID: 4bou | ||||||
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Title | Structure of OTUD3 OTU domain | ||||||
Components | OTU DOMAIN-CONTAINING PROTEIN 3 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information protein K6-linked deubiquitination / cysteine-type deubiquitinase activity => GO:0004843 / protein K27-linked deubiquitination / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 ...protein K6-linked deubiquitination / cysteine-type deubiquitinase activity => GO:0004843 / protein K27-linked deubiquitination / protein K11-linked deubiquitination / protein K48-linked deubiquitination / protein deubiquitination / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Regulation of PTEN stability and activity / Ovarian tumor domain proteases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 | 4bou.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bou.ent.gz | 55 KB | Display | PDB format |
PDBx/mmJSON format | 4bou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bou_validation.pdf.gz | 418.8 KB | Display | wwPDB validaton report |
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Full document | 4bou_full_validation.pdf.gz | 419.7 KB | Display | |
Data in XML | 4bou_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4bou_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/4bou ftp://data.pdbj.org/pub/pdb/validation_reports/bo/4bou | HTTPS FTP |
-Related structure data
Related structure data | 4bopC 4boqC 4bosC 4bozC 3pfyS 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: 18353.455 Da / Num. of mol.: 1 / Fragment: RESIDUES 52-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLACI / References: UniProt: Q5T2D3, ubiquitinyl hydrolase 1 |
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#2: Water | ChemComp-HOH / |
Sequence details | CONTAINS ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE |
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Crystal grow | Details: 10% PEG 4K, 0.1 M KCL, 0.01 M MGCL2, 50 MM MES PH 6.0 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97627 |
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: 0.97627 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→42.21 Å / Num. obs: 23429 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 23.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PFY Resolution: 1.55→31.347 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.01 / 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: 1.55→31.347 Å
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Refine LS restraints |
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LS refinement shell |
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