+Open data
-Basic information
Entry | Database: PDB / ID: 2g4m | ||||||
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Title | Insulin collected at 2.0 A wavelength | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR / insulin at 2.0 A wavelength / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Mueller-Dieckmann, C. / Weiss, M.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4m.cif.gz | 18.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4m.ent.gz | 15 KB | Display | PDB format |
PDBx/mmJSON format | 2g4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g4m_validation.pdf.gz | 410.4 KB | Display | wwPDB validaton report |
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Full document | 2g4m_full_validation.pdf.gz | 410.3 KB | Display | |
Data in XML | 2g4m_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 2g4m_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4m ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4m | HTTPS FTP |
-Related structure data
Related structure data | 2g4hC 2g4iC 2g4jC 2g4kC 2g4lC 2g4nC 2g4oC 2g4pC 2g4qC 2g4rC 2g4sC 2g4tC 2g4uC 2g4vC 2g4wC 2g4xC 2g4yC 2g4zC 2g51C 2g52C 2g55C 2illC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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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: 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: 3.45 Å3/Da / Density % sol: 64.36 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 7537 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.756 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.102 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.011 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 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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Refinement TLS params. | Method: refined / Origin x: 20.4067 Å / Origin y: 38.7807 Å / Origin z: 28.4551 Å
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Refinement TLS group |
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