+Open data
-Basic information
Entry | Database: PDB / ID: 5ejj | ||||||
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Title | Crystal structure of UfSP from C.elegans | ||||||
Components | Ufm1-specific protease | ||||||
Keywords | HYDROLASE / Ufm1 / UfSP / Deufmylation | ||||||
Function / homology | Function and homology information deUFMylase activity / protein localization to non-motile cilium / positive regulation of chemotaxis / chemotaxis / response to ethanol / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / endoplasmic reticulum membrane / perinuclear region of cytoplasm / protein-containing complex / proteolysis Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Kim, K. / Ha, B. / Kim, E.E. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2016 Title: The MPN domain of Caenorhabditis elegans UfSP modulates both substrate recognition and deufmylation activity Authors: Ha, B.H. / Kim, K.H. / Yoo, H.M. / Lee, W. / Kim, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ejj.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ejj.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ejj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ejj ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ejj | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 64095.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: odr-8, ufsp-2, F38A5.1 / Plasmid: pET28a / Cell line (production host): BL21RIL / Production host: Escherichia coli (E. coli) References: UniProt: Q94218, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.13 Å3/Da / Density % sol: 76.02 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Bicine, Ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2007 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 66417 / % possible obs: 93.8 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 1.65 / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.278 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 25.58 / 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: 2.8→41.278 Å
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Refine LS restraints |
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LS refinement shell |
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