+Open data
-Basic information
Entry | Database: PDB / ID: 5ubw | ||||||
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Title | Structure of catalytic domain of Ssel | ||||||
Components | Deubiquitinase SseL | ||||||
Keywords | HYDROLASE / UCH family / Salmonella / deubiquitinases | ||||||
Function / homology | cysteine-type peptidase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / Deubiquitinase SseL Function and homology information | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å | ||||||
Authors | Shrestha, R. / Das, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of catalytic domain of Ssel Authors: Shrestha, R. / Das, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ubw.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ubw.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ubw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ub/5ubw ftp://data.pdbj.org/pub/pdb/validation_reports/ub/5ubw | HTTPS FTP |
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-Related structure data
Related structure data | 5hafS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 21033.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: sseL, STM2287 / Production host: Escherichia coli (E. coli) References: UniProt: Q8ZNG2, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | ChemComp-EDO / | #3: 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: 2.35 Å3/Da / Density % sol: 47.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M HEPES sodium pH 7.5 and 1.5 M lithium sulfate monohydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.394→54.6 Å / Num. obs: 14585 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.394→2.44 Å / Redundancy: 3.8 % / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HAF Resolution: 2.394→42.604 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 34.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.394→42.604 Å
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Refine LS restraints |
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LS refinement shell |
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