[English] 日本語
Yorodumi- PDB-4ihn: High Resolution Insulin by Langmuir-Blodgett Modified Hanging Dro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ihn | ||||||
---|---|---|---|---|---|---|---|
Title | High Resolution Insulin by Langmuir-Blodgett Modified Hanging Drop Vapour Diffusion | ||||||
Components |
| ||||||
Keywords | HORMONE / Optimal Crystallization / Langmuir-Blodgett / Thin-Films | ||||||
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 / Resolution: 1.16 Å | ||||||
Authors | Belmonte, L. / Pechkova, E. / Bragazzi, N. / Nicolini, C. | ||||||
Citation | Journal: To be Published Title: A Review Of The Strategies For Obtaining High Quality Crystals Utilizing Nanotechnologies And Space Authors: Pechkova, E. / Bragazzi, N. / Bozdaganyan, M. / Belmonte, L.M. / Nicolini, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ihn.cif.gz | 19.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ihn.ent.gz | 15.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ihn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ihn_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ihn_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 4ihn_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 4ihn_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/4ihn ftp://data.pdbj.org/pub/pdb/validation_reports/ih/4ihn | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 2339.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Pancreas / References: UniProt: P01317 |
---|---|
#2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Pancreas / References: UniProt: P01317 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.73 % / Mosaicity: 0.14 ° |
---|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Type: ADSC QUANTUM 315r / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.158→55.395 Å / Num. all: 26153 / Num. obs: 26153 / % possible obs: 93.9 % / Redundancy: 2.8 % / Rsym value: 0.1 / Net I/σ(I): 8.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→55.39 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.3069 / WRfactor Rwork: 0.2816 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8305 / SU B: 0.559 / SU ML: 0.027 / SU R Cruickshank DPI: 0.041 / SU Rfree: 0.0439 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 53.03 Å2 / Biso mean: 17.7987 Å2 / Biso min: 6.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→55.39 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.158→1.188 Å / Total num. of bins used: 20
|