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Yorodumi- PDB-5d53: In meso in situ serial X-ray crystallography structure of insulin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d53 | ||||||
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Title | In meso in situ serial X-ray crystallography structure of insulin at 100 K | ||||||
Components |
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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 / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of protein secretion / hormone activity / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / positive regulation of cell migration / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Huang, C.-Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d53.cif.gz | 34.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d53.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 5d53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d53_validation.pdf.gz | 666.1 KB | Display | wwPDB validaton report |
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Full document | 5d53_full_validation.pdf.gz | 666 KB | Display | |
Data in XML | 5d53_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 5d53_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d53 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d53 | HTTPS FTP |
-Related structure data
Related structure data | 5d52C 5d54C 5d56C 5d57C 5d58C 5d59C 5d5aC 5d5bC 5d5cC 5d5dC 5d5eC 5d5fC 9insS 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/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: Chemical | #4: Chemical | ChemComp-PE5 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.31 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.1-0.2 M sodium phosphate, pH 5.5-6.1, and 33-38 %(w/v) PEG400 PH range: pH 5.5-6.1 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 13002 / % possible obs: 99.9 % / Redundancy: 6.4 % / Net I/σ(I): 9.08 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.21 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 9ins Resolution: 1.5→38.755 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.07 / 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: 1.5→38.755 Å
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Refine LS restraints |
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LS refinement shell |
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