[English] 日本語
Yorodumi- PDB-4idw: Polycrystalline T6 Bovine Insulin: Anisotropic Lattice Evolution ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4idw | ||||||
---|---|---|---|---|---|---|---|
Title | Polycrystalline T6 Bovine Insulin: Anisotropic Lattice Evolution and Novel Structure Refinement Strategy | ||||||
Components |
| ||||||
Keywords | HORMONE / INSULIN FAMILY / CARBOHYDRATE METABOLISM / HORMONE-GROWTH / T6 Bovine Insulin | ||||||
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 / response to food / feeding behavior / response to growth hormone / 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 | POWDER DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Margiolaki, I. / Giannopoulou, A.E. / Wright, J.P. / Knight, L. / Norrman, M. / Schluckebier, G. / Fitch, A. / Von Dreele, R.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: High-resolution powder X-ray data reveal the T6 hexameric form of bovine insulin Authors: Margiolaki, I. / Giannopoulou, A.E. / Wright, J.P. / Knight, L. / Norrman, M. / Schluckebier, G. / Fitch, A.N. / Von Dreele, R.B. | ||||||
History |
| ||||||
Remark 250 | REFINEMENT. PROGRAM : GSAS AUTHORS : LARSON & VON DREELE DATA USED IN REFINEMENT RESOLUTION RANGE ... REFINEMENT. PROGRAM : GSAS AUTHORS : LARSON & VON DREELE DATA USED IN REFINEMENT RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69 RESOLUTION RANGE LOW (ANGSTROMS) : 18.18 POWDER DIFFRACTION DATA. FIT TO DATA USED IN REFINEMENT NUMBER OF POWDER PATTERNS : 14 PROFILE R VALUES (%) : 7.06 7.85 8.54 7.50 9.13 WEIGHTED PROFILE R VALUES (%) : 9.37 10.00 11.16 9.44 11.37 F**2 R VALUES (%) : 25.05 31.98 18.03 35.26 33.68 NUMBERS OF POWDER PATTERN POINTS : 8999 8999 8999 6750 6750 NUMBERS OF REFLECTIONS : 2138 2118 2138 2138 2118 TOTAL NUMBER OF POWDER POINTS :120575 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. PROTEIN ATOMS : 800 NUCLEIC ACID ATOMS : NULL HETEROGEN ATOMS : 2 SOLVENT ATOMS : 44 MODEL REFINEMENT. NUMBER OF LEAST-SQUARES PARAMETERS : 1102 NUMBER OF RESTRAINTS : 1542 LEAST-SQUARES MATRIX BAND WIDTH : 50 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. NUMBER. BOND ANGLES (DEG) : 1.75 306 INTERATOMIC DISTANCES (A) :0.029 220 CHIRAL VOLUMES (A**3) :0.089 98 DISTANCES FROM RESTRAINT PLANES (A) :0.026 102 TORSION PSEUDOPOTENTIAL RESTRAINTS (E) : 3.49 135 TORSION ANGLE RESTRAINTS (E) : 0.84 290 ANTI-BUMPING DISTANCE RESTRAINTS (A) :0.505 286 HYDROGEN BOND DISTANCE RESTRAINTS (A) :0.119 80 EXPERIMENTAL DETAILS EXPERIMENT TYPE : X-RAY POWDER DIFFRACTION DATE OF DATA COLLECTION : 07-NOV-2006 TEMPERATURE (KELVIN) : 295 PH : NULL SAMPLE HOLDER : 1.0MM GLASS CAPILLARY NUMBER OF CRYSTALS USED : POLYCRYSTAL SLURRY SYNCHROTRON (Y/N) : Y RADIATION SOURCE : ESRF BEAMLINE : ID31, ID11 X-RAY GENERATOR MODEL : NULL MONOCHROMATIC OR LAUE (M/L) : M WAVELENGTH OR RANGE (A) : 1.29967(9), 0.53395(20) MONOCHROMATOR : DOUBLE SI(111) ANALYZER : SI(111) DETECTOR TYPE : NINE AVALANCHE PHOTODIODE (APD) DE DETECTOR MANUFACTURER : NULL INTENSITY-INTEGRATION SOFTWARE : NULL DATA SCALING/ INTEGRATION SOFTWARE : ID31SUM, FIT2D SOFTWARE USED: GSAS STARTING MODEL: NULL |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4idw.cif.gz | 28.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4idw.ent.gz | 21 KB | Display | PDB format |
PDBx/mmJSON format | 4idw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/4idw ftp://data.pdbj.org/pub/pdb/validation_reports/id/4idw | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein/peptide | Mass: 2339.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: POWDER DIFFRACTION |
---|
-Sample preparation
Crystal grow | Temperature: 295 K / Method: batch / pH: 6 Details: polycrystalline samples of T6 hexameric insulin (Zn2[(AB)2]3, the pH was adjusted by mixing different ratios of 0.2M solutions of sodium monobasic monohydrate phosphate and potassium ...Details: polycrystalline samples of T6 hexameric insulin (Zn2[(AB)2]3, the pH was adjusted by mixing different ratios of 0.2M solutions of sodium monobasic monohydrate phosphate and potassium phosphate., Batch, temperature 295K |
---|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1.29967, 0.53395 | ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.7→18.2 Å / Num. all: 2140 / Num. obs: 2140 / % possible obs: 70 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
-Processing
Software |
|
---|