+Open data
-Basic information
Entry | Database: PDB / ID: 5o71 | ||||||
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Title | Crystal structure of human USP25 | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 25 | ||||||
Keywords | HYDROLASE / Protease / de-ubiquinating Enzyme / USP family | ||||||
Function / homology | Function and homology information ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / protein modification process / regulation of protein stability / peptidase activity ...ubiquitin-like protein peptidase activity / negative regulation of ERAD pathway / SUMO binding / protein K48-linked deubiquitination / protein K63-linked deubiquitination / protein deubiquitination / ubiquitin binding / protein modification process / regulation of protein stability / peptidase activity / ATPase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / ubiquitin protein ligase binding / endoplasmic reticulum / proteolysis / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.283 Å | ||||||
Authors | Reverter, D. / Liu, B. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25. Authors: Liu, B. / Sureda-Gomez, M. / Zhen, Y. / Amador, V. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o71.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o71.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 5o71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o71 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o71 | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 82439.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP25, USP21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHP3, ubiquitinyl hydrolase 1 |
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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: 2.86 Å3/Da / Density % sol: 56.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 3.283→95.08 Å / Num. obs: 14883 / % possible obs: 99.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Rrim(I) all: 0.078 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 3.283→3.294 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 129 / Rpim(I) all: 0.626 / Rrim(I) all: 1.181 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.283→95.08 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.26 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.487 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 146.785 Å2
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Refinement step | Cycle: 1 / Resolution: 3.283→95.08 Å
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