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- PDB-4i5y: Insulin protein crystallization via langmuir-blodgett -

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Basic information

Entry
Database: PDB / ID: 4i5y
TitleInsulin protein crystallization via langmuir-blodgett
Components(Insulin) x 2
KeywordsHORMONE / langmuir blodgett / thin films / optimal crystallization / space grown
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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBelmonte, L. / Pechkova, E. / Bragazzi, N. / Nicolini, C.
CitationJournal: CRIT.REV.EUKARYOT.GENE EXPR. / Year: 2013
Title: A Review OF THE STRATEGIES FOR OBTAINING HIGH QUALITY CRYSTALS UTILIZING NANOTECHNOLOGIES AND SPACE
Authors: Pechkova, E. / Bragazzi, N. / Belmonte, L. / Nicolini, C.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7442
Polymers5,7442
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-15 kcal/mol
Surface area3390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.200, 78.200, 78.200
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-104-

HOH

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Components

#1: Protein/peptide Insulin / / Insulin B chain / Insulin A chain


Mass: 2339.645 Da / Num. of mol.: 1 / Fragment: UNP residues 85-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01317
#2: Protein/peptide Insulin / / Insulin B chain / Insulin A chain


Mass: 3403.927 Da / Num. of mol.: 1 / Fragment: UNP residues 25-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01317
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.47 Å3/Da / Density % sol: 64.54 % / Mosaicity: 0.19 °

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.932 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.8→55.3 Å / Num. all: 7540 / Num. obs: 7540 / % possible obs: 99.9 % / Redundancy: 21.1 % / Rsym value: 0.097 / Net I/σ(I): 25.1
Reflection shell

Num. measured obs: 10 / 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
1.8-1.920.70.350.3412.12288511030.0770.350.3419.8100
1.9-2.0120.50.2570.2512.72092510230.0570.2570.25113.1100
2.01-2.1519.40.180.1764186739640.0410.180.17617.1100
2.15-2.3220.70.1430.143.9186038990.0310.1430.1421.7100
2.32-2.5522.20.1120.1095.8185868380.0240.1120.10927.1100
2.55-2.8522.40.0940.0926.7168107520.020.0940.09231.9100
2.85-3.2922.10.0810.087.6150966820.0170.0810.0837.7100
3.29-4.03220.0710.078124525660.0150.0710.0744.4100
4.03-5.6921.50.070.0698.197624550.0150.070.06946.2100
5.69-20.920.10.0660.0648.651912580.0150.0660.06441.398.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.91 Å20.9 Å
Translation1.91 Å20.9 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→55.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.1789 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8601 / SU B: 2.118 / SU ML: 0.066 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 345 4.6 %RANDOM
Rwork0.1822 ---
obs0.1841 7507 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.22 Å2 / Biso mean: 18.8425 Å2 / Biso min: 5.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 0 52 452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022411
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.952558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.342549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29224.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8161562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.734151
X-RAY DIFFRACTIONr_chiral_restr0.1690.260
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02318
X-RAY DIFFRACTIONr_mcbond_it1.7731.5252
X-RAY DIFFRACTIONr_mcangle_it3.0842401
X-RAY DIFFRACTIONr_scbond_it3.7713159
X-RAY DIFFRACTIONr_scangle_it5.7484.5157
LS refinement shellResolution: 1.8→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 17 -
Rwork0.224 539 -
all-556 -
obs--100 %

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