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Yorodumi- PDB-4pqt: Insights into the mechanism of deubiquitination by JAMM deubiquit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pqt | ||||||
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Title | Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal structures of enzyme with substrate and product | ||||||
Components |
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Keywords | Hydrolase/transcription / helix-beta-helix sandwich / ubiquitin / deubiquitination / Zinc metalloprotease / Lysine 63-linked polyubiquitin / Hydrolase-transcription complex | ||||||
Function / homology | Function and homology information Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site / ubiquitin binding / endosome / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Shrestha, R.K. / Ronau, J.A. / Das, C. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product. Authors: Shrestha, R.K. / Ronau, J.A. / Davies, C.W. / Guenette, R.G. / Strieter, E.R. / Paul, L.N. / Das, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pqt.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pqt.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/4pqt ftp://data.pdbj.org/pub/pdb/validation_reports/pq/4pqt | HTTPS FTP |
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-Related structure data
Related structure data | 4jxeC 4k1rSC 4ms7C 4msdC 4msjC 4msmC 4msqC 4nqlC 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 21937.723 Da / Num. of mol.: 1 / Fragment: Catalytic domain unp residues 245-435 / Mutation: D354A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / ATCC 24843 / Gene: SPAC19B12.10, sst2 / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases | ||
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#2: Protein | Mass: 8988.284 Da / Num. of mol.: 1 / Fragment: unp residues 77-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBBP4, Ubiquitin / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: J3QRK5 | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-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: 41.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1% w/v Tryptone, 0.05M HEPES sodium, 20% PEG 3,350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2013 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→60 Å / Num. all: 16438 / Num. obs: 16438 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.05→2.05 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.625 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4K1R Resolution: 2.05→40.109 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.59 / 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: 2.05→40.109 Å
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Refine LS restraints |
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LS refinement shell |
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