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- PDB-4ihn: High Resolution Insulin by Langmuir-Blodgett Modified Hanging Dro... -

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Basic information

Entry
Database: PDB / ID: 4ihn
TitleHigh Resolution Insulin by Langmuir-Blodgett Modified Hanging Drop Vapour Diffusion
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Optimal Crystallization / Langmuir-Blodgett / Thin-Films
Function / homology
Function and homology information


glucose import in response to insulin stimulus / response to butyrate / positive regulation of blood circulation / negative regulation of lactation / estradiol secretion / positive regulation of lactation / positive regulation of cell maturation / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to L-arginine ...glucose import in response to insulin stimulus / response to butyrate / positive regulation of blood circulation / negative regulation of lactation / estradiol secretion / positive regulation of lactation / positive regulation of cell maturation / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to L-arginine / feeding behavior / response to food / positive regulation of Rho protein signal transduction / response to growth hormone / positive regulation of peptide hormone secretion / protein secretion / positive regulation of insulin secretion / negative regulation of lipid catabolic process / positive regulation of protein secretion / response to glucose / response to nutrient levels / hormone activity / insulin receptor binding / glucose metabolic process / response to heat / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin-like superfamily / Insulin family signature.
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsBelmonte, L. / Pechkova, E. / Bragazzi, N. / Nicolini, C.
CitationJournal: 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
DepositionDec 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release

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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


Theoretical massNumber of molelcules
Total (without water)5,7442
Polymers5,7442
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-15 kcal/mol
Surface area3380 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.340, 78.340, 78.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-111-

HOH

21B-123-

HOH

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Components

#1: Protein/peptide Insulin A chain


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 Insulin B chain


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 / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.73 % / Mosaicity: 0.14 °

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.16-1.222.80.1690.1383.51115540140.0940.1690.1386.499.7
1.22-1.292.80.130.1075.91078338310.0730.130.1077.499.9
1.29-1.382.80.1210.0993.21025036120.0680.1210.0998.499.8
1.38-1.52.80.1170.0955.6948733460.0670.1170.0959.499.9
1.5-1.642.80.1090.0896.2872930800.0620.1090.0891099.9
1.64-1.832.80.1090.0896.1797727990.0620.1090.08910.599.6
1.83-2.112.80.1380.1115.1686624740.080.1380.11110.599.6
2.11-2.592.50.1270.16.2485919100.0760.1270.110.191
2.59-3.662.30.1180.0937.220799010.0710.1180.0939.654.1
3.66-19.5852.20.1250.16.74071860.0740.1250.19.418.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1314 5 %RANDOM
Rwork0.233 ---
obs0.2343 26104 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.03 Å2 / Biso mean: 17.7987 Å2 / Biso min: 6.01 Å2
Refinement stepCycle: LAST / Resolution: 1.16→55.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 0 86 486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.022411
X-RAY DIFFRACTIONr_angle_refined_deg2.3291.952558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.157549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.91724.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3811562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.515151
X-RAY DIFFRACTIONr_chiral_restr0.1630.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02318
X-RAY DIFFRACTIONr_mcbond_it1.6451.5252
X-RAY DIFFRACTIONr_mcangle_it2.8762401
X-RAY DIFFRACTIONr_scbond_it3.43159
X-RAY DIFFRACTIONr_scangle_it4.1924.5157
LS refinement shellResolution: 1.158→1.188 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 101 -
Rwork0.283 1917 -
all-2018 -
obs--98.97 %

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