+Open data
-Basic information
Entry | Database: PDB / ID: 4mem | ||||||
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Title | Crystal Structure of the rat USP11 DUSP-UBL domains | ||||||
Components | Ubiquitin carboxyl-terminal hydrolase 11 | ||||||
Keywords | HYDROLASE / DOMAIN PRESENT IN UBIQUITIN SPECIFIC PROTEASES (DUSP) / UBIQUITIN-LIKE DOMAIN (UBL) / DU FINGER / UBIQUITIN THIOLESTERASE / DEUBIQUITINATING ENZYME (DUB) | ||||||
Function / homology | Function and homology information transcription corepressor binding => GO:0001222 / Ub-specific processing proteases / protein deubiquitination / chromosome / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Harper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structure and Catalytic Regulatory Function of Ubiquitin Specific Protease 11 N-Terminal and Ubiquitin-like Domains. Authors: Harper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mem.cif.gz | 187.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mem.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 4mem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/4mem ftp://data.pdbj.org/pub/pdb/validation_reports/me/4mem | HTTPS FTP |
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-Related structure data
Related structure data | 4melSC S: Starting model for refinement C: citing same article (ref.) |
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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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3 |
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Unit cell |
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Details | biological assembly is a monomer. There are 2 biological units in the asymmetric unit (chain A chain B). |
-Components
#1: Protein | Mass: 26465.500 Da / Num. of mol.: 2 / Fragment: DUSP-UBL domains, UNP residues 19-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: 10116 / Gene: rCG_42884, Usp11 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5D006, ubiquitinyl hydrolase 1 #2: 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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.77 Details: 0.15 M Malic Acid, 24% w/v PEG 3350, 10 mM Strontium Chloride, pH 6.77, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 2.292→74.635 Å / Num. obs: 20914 / % possible obs: 99.7 % / Redundancy: 11.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4MEL Resolution: 2.34→54.622 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.31 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 28 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.9952 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.34→54.622 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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