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- PDB-4idw: Polycrystalline T6 Bovine Insulin: Anisotropic Lattice Evolution ... -

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Basic information

Entry
Database: PDB / ID: 4idw
TitlePolycrystalline T6 Bovine Insulin: Anisotropic Lattice Evolution and Novel Structure Refinement Strategy
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / 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
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodPOWDER DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsMargiolaki, I. / Giannopoulou, A.E. / Wright, J.P. / Knight, L. / Norrman, M. / Schluckebier, G. / Fitch, A. / Von Dreele, R.B.
CitationJournal: 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
DepositionDec 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A chain
B: Insulin B chain
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6186
Polymers11,4874
Non-polymers1312
Water79344
1
A: Insulin A chain
B: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
hetero molecules

A: Insulin A chain
B: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4279
Polymers17,2316
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5390 Å2
ΔGint-98 kcal/mol
Surface area10970 Å2
MethodPISA
2
C: Insulin A chain
D: Insulin B chain
hetero molecules

C: Insulin A chain
D: Insulin B chain
hetero molecules

C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4279
Polymers17,2316
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5680 Å2
ΔGint-100 kcal/mol
Surface area10440 Å2
MethodPISA
Components on special symmetry positions
IDModelComponents
11B-501-

ZN

21D-101-

ZN

31B-611-

HOH

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Components

#1: Protein/peptide Insulin A chain


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 Insulin B chain


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 ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: POWDER DIFFRACTION

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Sample preparation

Crystal growTemperature: 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12951
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 1.29967, 0.53395
Detector
TypeIDDetectorDateDetails
Frelon4M 2k x 2k CCD camera1CCDNov 7, 2006DOUBLE SI(111) monochromator
APD2NINE AVALANCHE PHOTODIODE (APD) DETECTORS (SI BASED)Nov 7, 2006DOUBLE SI(111)monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE SI(111)SINGLE WAVELENGTHMx-ray1
2DOUBLE SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.299671
20.533951
ReflectionResolution: 2.7→18.2 Å / Num. all: 2140 / Num. obs: 2140 / % possible obs: 70 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameClassification
ID31sumdata collection
MOLREPphasing
GSASrefinement
FIT2Ddata reduction
ID31sumdata scaling

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