+Open data
-Basic information
Entry | Database: PDB / ID: 6qrk | ||||||
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Title | High pressure structure of bovine insulin (200 MPa) | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE / glucose metabolism | ||||||
Function / homology | Function and homology information estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate ...estradiol secretion / negative regulation of lactation / positive regulation of blood circulation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to butyrate / feeding behavior / response to growth hormone / response to food / positive regulation of Rho protein signal transduction / positive regulation of peptide hormone secretion / protein secretion / negative regulation of lipid catabolic process / response to glucose / response to nutrient levels / positive regulation of protein secretion / insulin receptor binding / positive regulation of insulin secretion / hormone activity / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.102 Å | ||||||
Authors | Kurpiewska, K. / Milaczewska, A. / Lewinski, K. | ||||||
Citation | Journal: J.Mol.Struct. / Year: 2020 Title: Insulin conformational changes under high pressure in structural studies and molecular dynamics simulations Authors: Kurpiewska, K. / Milaczewska, A. / Lewinski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qrk.cif.gz | 22.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qrk.ent.gz | 13.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qrk_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 6qrk_full_validation.pdf.gz | 422.3 KB | Display | |
Data in XML | 6qrk_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | 6qrk_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/6qrk ftp://data.pdbj.org/pub/pdb/validation_reports/qr/6qrk | HTTPS FTP |
-Related structure data
Related structure data | 6qq7C 6qqgC 6qrhC 2bn3S 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
#1: Protein/peptide | Mass: 2339.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 |
#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: 3.46 Å3/Da / Density % sol: 64.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 0.01 Na3EDTA, 0.1 MNa2HEDTA |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 0.7107 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 16, 2011 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7107 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→16.66 Å / Num. obs: 4702 / % possible obs: 99 % / Redundancy: 1.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.127 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.454 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BN3 Resolution: 2.102→15.95 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.88 / 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: 2.102→15.95 Å
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Refine LS restraints |
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LS refinement shell |
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