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- PDB-4msj: Crystal structure of S. pombe AMSH-like protease SST2 catalytic d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4msj | ||||||
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Title | Crystal structure of S. pombe AMSH-like protease SST2 catalytic domain from P212121 space group | ||||||
![]() | AMSH-like protease sst2 | ||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shrestha, R.K. / Ronau, J.A. / Das, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.7 KB | Display | ![]() |
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PDB format | ![]() | 101.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4jxeSC ![]() 4k1rC ![]() 4ms7C ![]() 4msdC ![]() 4msmC ![]() 4msqC ![]() 4nqlC ![]() 4pqtC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 21981.732 Da / Num. of mol.: 3 / Fragment: catalytic domain, UNP residues 245-435 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: 972/ATCC 24843 / Gene: sst2, SPAC19B12.10 / Plasmid: pGEX-6P-1 / Production host: ![]() ![]() ![]() References: UniProt: Q9P371, ![]() |
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-Non-polymers , 5 types, 236 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-GLY / | ![]() #5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M ammonium phosphate dibasic, 20% w/v PEG 3350, 1.0 M glycine, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2012 |
Radiation | Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→50 Å / Num. all: 56615 / Num. obs: 55256 / % possible obs: 97.9 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.628 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB CODE 4JXE Resolution: 1.8→47.31 Å / SU ML: 0.19 / σ(F): 1.37 / Phase error: 23.66 / 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: 1.8→47.31 Å
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Refine LS restraints |
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LS refinement shell |
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