+Open data
-Basic information
Entry | Database: PDB / ID: 4i5y | ||||||
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Title | Insulin protein crystallization via langmuir-blodgett | ||||||
Components | (Insulin) x 2 | ||||||
Keywords | HORMONE / langmuir blodgett / thin films / optimal crystallization / space grown | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Belmonte, L. / Pechkova, E. / Bragazzi, N. / Nicolini, C. | ||||||
Citation | Journal: CRIT.REV.EUKARYOT.GENE EXPR. / Year: 2013 Title: A Review OF THE STRATEGIES FOR OBTAINING HIGH QUALITY CRYSTALS UTILIZING NANOTECHNOLOGIES AND SPACE Authors: Pechkova, E. / Bragazzi, N. / Belmonte, L. / Nicolini, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i5y.cif.gz | 19.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i5y.ent.gz | 14.6 KB | Display | PDB format |
PDBx/mmJSON format | 4i5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i5y_validation.pdf.gz | 422.4 KB | Display | wwPDB validaton report |
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Full document | 4i5y_full_validation.pdf.gz | 422.4 KB | Display | |
Data in XML | 4i5y_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 4i5y_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/4i5y ftp://data.pdbj.org/pub/pdb/validation_reports/i5/4i5y | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 2339.645 Da / Num. of mol.: 1 / Fragment: UNP residues 85-105 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01317 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Fragment: UNP residues 25-54 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: INS / Production host: Escherichia coli (E. coli) / 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: 3.47 Å3/Da / Density % sol: 64.54 % / Mosaicity: 0.19 ° |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.932 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→55.3 Å / Num. all: 7540 / Num. obs: 7540 / % possible obs: 99.9 % / Redundancy: 21.1 % / Rsym value: 0.097 / Net I/σ(I): 25.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Num. measured obs: 10 / Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→55.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.1789 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8601 / SU B: 2.118 / SU ML: 0.066 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.102 / 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 max: 62.22 Å2 / Biso mean: 18.8425 Å2 / Biso min: 5.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→55.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.849 Å / Total num. of bins used: 20
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