+Open data
-Basic information
Entry | Database: PDB / ID: 4a3o | ||||||
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Title | Crystal structure of the USP15 DUSP-UBL monomer | ||||||
Components | UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15 | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / protein deubiquitination / SMAD binding / BMP signaling pathway / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Elliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L. | ||||||
Citation | Journal: FEBS Lett. / Year: 2011 Title: Structural Variability of the Ubiquitin Specific Protease Dusp-Ubl Double Domains. Authors: Elliott, P.R. / Liu, H. / Pastok, M.W. / Grossmann, G.J. / Rigden, D.J. / Clague, M.J. / Urbe, S. / Barsukov, I.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a3o.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a3o.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 4a3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/4a3o ftp://data.pdbj.org/pub/pdb/validation_reports/a3/4a3o | HTTPS FTP |
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-Related structure data
Related structure data | 3pv1SC 4a3pC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (1, 0.00112, 0.001048), Vector: |
-Components
#1: Protein | Mass: 25510.793 Da / Num. of mol.: 2 / Fragment: DUSP-UBL, RESIDUES 4-233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y4E8, ubiquitinyl hydrolase 1 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 4.1 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.9 M (NH4)2SO4, 100 MM HEPES PH 7.0, 200 MM KI |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→55.03 Å / Num. obs: 61255 / % possible obs: 99 % / Observed criterion σ(I): 2.3 / Redundancy: 2.9 % / Biso Wilson estimate: 30.95 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PV1 Resolution: 2.2→55.324 Å / SU ML: 0.31 / σ(F): 1.97 / Phase error: 23.71 / 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 / Bsol: 37.843 Å2 / ksol: 0.386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→55.324 Å
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Refine LS restraints |
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LS refinement shell |
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