+Open data
-Basic information
Entry | Database: PDB / ID: 3ca7 | ||||||
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Title | High Resolution Crystal Structure of the EGF domain of Spitz | ||||||
Components | Protein spitz | ||||||
Keywords | HORMONE/SIGNALING PROTEIN / Spitz / Argos / EGF / Developmental protein / Differentiation / EGF-like domain / Endoplasmic reticulum / Glycoprotein / Golgi apparatus / Membrane / Neurogenesis / Transmembrane / HORMONE-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information ectodermal cell fate determination / stomatogastric nervous system development / stem cell fate commitment / photoreceptor cell fate determination / photoreceptor cell differentiation / epithelial cell proliferation involved in Malpighian tubule morphogenesis / determination of genital disc primordium / ommatidial rotation / oenocyte development / dorsal closure ...ectodermal cell fate determination / stomatogastric nervous system development / stem cell fate commitment / photoreceptor cell fate determination / photoreceptor cell differentiation / epithelial cell proliferation involved in Malpighian tubule morphogenesis / determination of genital disc primordium / ommatidial rotation / oenocyte development / dorsal closure / spiracle morphogenesis, open tracheal system / border follicle cell migration / positive regulation of border follicle cell migration / imaginal disc-derived wing morphogenesis / behavioral response to ethanol / heart process / olfactory learning / peripheral nervous system development / positive regulation of neurogenesis / epidermal growth factor receptor binding / transmembrane receptor protein tyrosine kinase activator activity / epidermal growth factor receptor signaling pathway / receptor ligand activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / extracellular space / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Klein, D.E. / Stayrook, S.E. / Lemmon, M.A. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structural basis for EGFR ligand sequestration by Argos. Authors: Klein, D.E. / Stayrook, S.E. / Shi, F. / Narayan, K. / Lemmon, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ca7.cif.gz | 24.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ca7.ent.gz | 14.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ca7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3ca7 ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3ca7 | HTTPS FTP |
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-Related structure data
Related structure data | 3c9aC 3cguC 1jl9S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 6012.862 Da / Num. of mol.: 1 / Fragment: UNP residues 76-127 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spi / Plasmid: pMT/BiP/V5-HisA(Invitrogen) / Cell (production host): Schneider-2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q01083 |
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#2: 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: 2.17 Å3/Da / Density % sol: 43.19 % |
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Crystal grow | Temperature: 294 K / pH: 6.5 Details: 15mM ammonium sulphate, 0.1M MES pH 6.5, 24% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 294K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.92 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2007 / Details: 3.0 UNDULATOR |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.499→50 Å / Num. obs: 7284 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.499→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4.6 / % possible all: 56.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JL9 Resolution: 1.5→30.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.273 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / 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: 20.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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