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Yorodumi- PDB-4msd: Crystal structure of Schizosaccharomyces pombe AMSH-like protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4msd | ||||||
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Title | Crystal structure of Schizosaccharomyces pombe AMSH-like protein SST2 T319I mutant | ||||||
Components | AMSH-like protease sst2 | ||||||
Keywords | HYDROLASE / Helix-beta-helix sandwich / ubiquitin / deubiquitination / zinc metalloprotease / AMSH / lysine 63-linked polyubiquitin / cytosol | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 4msd.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4msd.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 4msd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4msd_validation.pdf.gz | 467.5 KB | Display | wwPDB validaton report |
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Full document | 4msd_full_validation.pdf.gz | 469.1 KB | Display | |
Data in XML | 4msd_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4msd_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/4msd ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4msd | HTTPS FTP |
-Related structure data
Related structure data | 4jxeSC 4k1rC 4ms7C 4msjC 4msmC 4msqC 4nqlC 4pqtC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21993.787 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 245-435 / Mutation: T319I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972/ATCC 24843 / Gene: sst2, SPAC19B12.10 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-DTT / | #5: 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: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.03 M citric acid, 0.07 M bis-tris propane, pH 7.6, 20% PEG 3350, benzamidine hydrochloride (additive), 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-B / Wavelength: 1.033 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 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: 1.9→50 Å / Num. all: 39816 / Num. obs: 39816 / % possible obs: 100 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1996 / Rsym value: 0.565 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 4JXE Resolution: 1.9→33.612 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.02 / 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: 1.9→33.612 Å
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Refine LS restraints |
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LS refinement shell |
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