+Open data
-Basic information
Entry | Database: PDB / ID: 4zd5 | ||||||
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Title | Catalytic domain of Sst2 F403A mutant | ||||||
Components | AMSH-like protease sst2 | ||||||
Keywords | HYDROLASE / helix-beta-helix sandwich Zinc metalloprotease endosome Ubiquitin | ||||||
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: 2.07 Å | ||||||
Authors | Shrestha, R.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of the catalytic domain of Sst2 F403A mutant at 2.07 Angstoms resolution Authors: Shrestha, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zd5.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zd5.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 4zd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zd5_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 4zd5_full_validation.pdf.gz | 453.2 KB | Display | |
Data in XML | 4zd5_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 4zd5_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/4zd5 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/4zd5 | HTTPS FTP |
-Related structure data
Related structure data | 4ms7S S: Starting model for refinement |
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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: 21905.637 Da / Num. of mol.: 2 / Fragment: unp residues 245-435 / Mutation: F403A 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 / Details (production host): 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: 0.2M sodium citrate tribasic diehydrate, 20%w/v PEG 3350 |
-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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2014 |
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: 2.07→59.5 Å / Num. obs: 31003 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.02 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MS7 Resolution: 2.07→59.49 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.021 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.592 Å2
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Refinement step | Cycle: 1 / Resolution: 2.07→59.49 Å
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