+Open data
-Basic information
Entry | Database: PDB / ID: 3qwx | ||||||
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Title | CED-2 1-174 | ||||||
Components | Cell death abnormality protein 2 | ||||||
Keywords | SIGNALING PROTEIN / Cell Engulfment | ||||||
Function / homology | Function and homology information positive regulation of distal tip cell migration / Frs2-mediated activation / : / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / positive regulation of engulfment of apoptotic cell / engulfment of apoptotic cell ...positive regulation of distal tip cell migration / Frs2-mediated activation / : / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / Regulation of signaling by CBL / positive regulation of engulfment of apoptotic cell / engulfment of apoptotic cell / apoptotic process involved in development / programmed cell death / signaling adaptor activity / receptor tyrosine kinase binding / cell migration / actin cytoskeleton organization / apoptotic process / protein-containing complex binding / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.01 Å | ||||||
Authors | Kang, Y. / Sun, J. / Liu, Y. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2011 Title: Crystal structure of the cell corpse engulfment protein CED-2 in Caenorhabditis elegans. Authors: Kang, Y. / Xu, J. / Liu, Y. / Sun, J. / Sun, D. / Hu, Y. / Liu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qwx.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qwx.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/3qwx ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qwx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19565.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ced-2, Y41D4B.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NHC3 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.44 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.2M lithium sulfate, 25% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→75.07 Å / Num. obs: 13490 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.01→38.86 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R Free: 0.184 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.174 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→38.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.061 Å / Total num. of bins used: 20
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