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Yorodumi- PDB-7fsj: SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7fsj | ||||||
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Title | SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z57744712 | ||||||
Components | Syntenin-1 | ||||||
Keywords | SIGNALING PROTEIN / Diamond I04-1 fragment screening / PanDDA / XChemExplorer | ||||||
Function / homology | Function and homology information interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / presynapse assembly / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion ...interleukin-5 receptor complex / interleukin-5 receptor binding / positive regulation of extracellular exosome assembly / syndecan binding / neurexin family protein binding / presynapse assembly / Neurofascin interactions / cytoskeletal anchor activity / substrate-dependent cell migration, cell extension / positive regulation of exosomal secretion / frizzled binding / negative regulation of receptor internalization / protein targeting to membrane / Ephrin signaling / RIPK1-mediated regulated necrosis / growth factor binding / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / positive regulation of phosphorylation / cell adhesion molecule binding / regulation of mitotic cell cycle / phosphatidylinositol-4,5-bisphosphate binding / protein sequestering activity / ephrin receptor binding / ionotropic glutamate receptor binding / adherens junction / positive regulation of JNK cascade / Regulation of necroptotic cell death / azurophil granule lumen / extracellular vesicle / melanosome / presynapse / actin cytoskeleton organization / positive regulation of cell growth / nuclear membrane / chemical synaptic transmission / Ras protein signal transduction / blood microparticle / cytoskeleton / intracellular signal transduction / positive regulation of cell migration / protein heterodimerization activity / membrane raft / focal adhesion / Neutrophil degranulation / positive regulation of cell population proliferation / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.97 Å | ||||||
Authors | Bradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: SDCBP PanDDA analysis group deposition Authors: Bradshaw, W.J. / Katis, V.L. / Bountra, C. / von Delft, F. / Brennan, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fsj.cif.gz | 168.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fsj.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 7fsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fsj_validation.pdf.gz | 874 KB | Display | wwPDB validaton report |
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Full document | 7fsj_full_validation.pdf.gz | 881.2 KB | Display | |
Data in XML | 7fsj_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 7fsj_validation.cif.gz | 48.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/7fsj ftp://data.pdbj.org/pub/pdb/validation_reports/fs/7fsj | HTTPS FTP |
-Group deposition
ID | G_1002262 (34 entries) |
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Title | SDCBP PanDDA analysis group deposition |
Type | changed state |
Description | XDomainX of XOrganismX SDCBP screened against the XXX Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 8bluS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21430.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SDCBP, MDA9, SYCL / Production host: Escherichia coli (E. coli) / References: UniProt: O00560 |
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-Non-polymers , 7 types, 411 molecules
#2: Chemical | ChemComp-YEB / | ||||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ALA / | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.68 Å3/Da / Density % sol: 54.19 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM Morpheus amino acids, 100 mM Morpheus buffer system 1, 43% Morpheus precipitant mix 3 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→114.54 Å / Num. obs: 64393 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.098 / Rrim(I) all: 0.184 / Net I/σ(I): 9 / Num. measured all: 223322 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 8BLU Resolution: 1.97→114.49 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.801 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.196 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 127.37 Å2 / Biso mean: 41.469 Å2 / Biso min: 22.63 Å2
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Refinement step | Cycle: final / Resolution: 1.97→114.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.973→2.024 Å / Total num. of bins used: 20
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