+Open data
-Basic information
Entry | Database: PDB / ID: 2bn1 | ||||||
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Title | Insulin after a high dose x-ray burn | ||||||
Components |
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Keywords | HORMONE / RADIATION DAMAGE / PHASING / RIP / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / 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 / 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 / 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.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bn1.cif.gz | 33 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bn1.ent.gz | 26.7 KB | Display | PDB format |
PDBx/mmJSON format | 2bn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bn1_validation.pdf.gz | 423.2 KB | Display | wwPDB validaton report |
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Full document | 2bn1_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 2bn1_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 2bn1_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/2bn1 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/2bn1 | HTTPS FTP |
-Related structure data
Related structure data | 2bloC 2blpC 2blqC 2blrC 2bluC 2blvC 2blwC 2blxC 2blyC 2blzC 2bn3C 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: 2339.645 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: 2.73 Å3/Da / Density % sol: 54.62 % |
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Crystal grow | Details: .4 M NAPO4/NA2HPO4 PH10.4, 0.001M 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): 18.99 |
Reflection shell | Resolution: 1.5→1.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.12 / % possible all: 95.9 |
-Processing
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Refinement | Method to determine structure: OTHER / Resolution: 1.4→45 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.493 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES GLU 4, GLN 15, ASN 18 AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES GLU 4, GLN 15, ASN 18 AND ASN 21 OF CHAIN A AND VAL 2, GLN 4, GLU 21, LYS 29 AND ALA 30 OF CHAIN B
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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: 14.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→45 Å
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