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Yorodumi- PDB-5fb6: Room-temperature macromolecular crystallography using a micro-pat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fb6 | |||||||||
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Title | Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering | |||||||||
Components |
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Keywords | HORMONE / cubic insulin | |||||||||
Function / homology | Function and homology information Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of DNA replication / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | |||||||||
Authors | Roedig, P. / Duman, R. / Sanchez-Weatherby, J. / Vartiainen, I. / Burkhardt, A. / Warmer, M. / David, C. / Wagner, A. / Meents, A. | |||||||||
Funding support | Switzerland, Germany, 2items
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Citation | Journal: J.Appl.Crystallogr. / Year: 2016 Title: Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering. Authors: Roedig, P. / Duman, R. / Sanchez-Weatherby, J. / Vartiainen, I. / Burkhardt, A. / Warmer, M. / David, C. / Wagner, A. / Meents, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fb6.cif.gz | 23.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fb6.ent.gz | 14.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fb6 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fb6 | HTTPS FTP |
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-Related structure data
Related structure data | 9insS 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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Unit cell |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.6 M Na2HPO4 0.01 M EDTA / PH range: 9.8 - 10.4 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.003 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2015 |
Radiation | Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.003 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 6542 / % possible obs: 99.21 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.05801 / Net I/σ(I): 18.04 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 5.16 / % possible all: 99.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 9INS Resolution: 1.901→27.867 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.36 / 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: 1.901→27.867 Å
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Refine LS restraints |
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LS refinement shell |
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