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Yorodumi- PDB-3rto: Acoustically mounted porcine insulin microcrystals yield an X-ray... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rto | ||||||
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Title | Acoustically mounted porcine insulin microcrystals yield an X-ray SAD structure | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE | ||||||
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 / positive regulation of DNA replication / 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 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 / SAD / Resolution: 1.8 Å | ||||||
Authors | Soares, A.S. / Engel, M.A. / Stearns, R. / Datwani, S. / Olechno, J. / Ellson, R. / Skinner, J.M. / Allaire, M. / Orville, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Acoustically Mounted Microcrystals Yield High-Resolution X-ray Structures. Authors: Soares, A.S. / Engel, M.A. / Stearns, R. / Datwani, S. / Olechno, J. / Ellson, R. / Skinner, J.M. / Allaire, M. / Orville, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rto.cif.gz | 34.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rto.ent.gz | 24.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rt/3rto ftp://data.pdbj.org/pub/pdb/validation_reports/rt/3rto | HTTPS FTP |
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-Related structure data
Related structure data | 4insS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: Insulin A chain (UNP residues 88-108) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: Insulin B chain (UNP residues 25-54) / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 9 |
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-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.42 % |
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Crystal grow | Method: small tubes / pH: 6 Details: Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc ...Details: Microcrystals are obtained by dissolving 0.025 g protein in 5 mL of crystallizing solution (200 mL 0.02 M HCl, 100 mL 0.20 M sodium citrate, 60 mL acetone, 20 mL water, 20 mL 0.12 M zinc sulfate) at 315K. The solution is then rapidly quenched to 293K by immersing it in a cool water bath. Quenching speed determines the resulting crystal size. 20-micron crystals are obtained by quenching in a 293K water bath, 10-micron crystals by quenching in a 283K water bath, and 5-micron crystals by quenching in ice water. pH 6.0, SMALL TUBES |
-Data collection
Diffraction |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.8→50 Å / Num. all: 7783 / Num. obs: 7770 / % possible obs: 99.8 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 62.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 4INS Resolution: 1.8→40.85 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.454 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.143 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.509 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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