+Open data
-Basic information
Entry | Database: PDB / ID: 2bn3 | ||||||
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Title | Insulin before a high dose x-ray burn | ||||||
Components | (INSULIN) x 2 | ||||||
Keywords | RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / HORMONE / INSULIN FAMILY | ||||||
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 / response to glucose / negative regulation of lipid catabolic process / response to nutrient levels / positive regulation of protein secretion / insulin receptor binding / hormone activity / positive regulation of insulin secretion / 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 / OTHER / Resolution: 1.4 Å | ||||||
Authors | Nanao, M.H. / Ravelli, R.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Improving Radiation-Damage Substructures for Rip. Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bn3.cif.gz | 33.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bn3.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bn3 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bn3 | HTTPS FTP |
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-Related structure data
Related structure data | 2bloC 2blpC 2blqC 2blrC 2bluC 2blvC 2blwC 2blxC 2blyC 2blzC 2bn1C 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: 2369.671 Da / Num. of mol.: 1 / Fragment: INSULIN A CHAIN, RESIDUES 85-105 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P01317 |
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#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Fragment: INSULIN B CHAIN, RESIDUES 25-54 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: PANCREAS / References: UniProt: P01317 |
#3: Water | ChemComp-HOH / |
Compound details | INSULIN DECREASES BLOOD GLUCOSE CONCENTRATION. IT INCREASES CELL PERMEABILITY TO MONOSACCHARIDES, ...INSULIN DECREASES BLOOD GLUCOSE CONCENTRAT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.51 % |
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Crystal grow | Details: 0.4 M NAPO4/NA2HPO4 PH 10.4, 0.001 M EDTA,30%ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9392 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 24081 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.98 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.401 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.043 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45 Å
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