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- PDB-4bs3: Bovin insulin structure determined by in situ crystal analysis an... -

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Basic information

Entry
Database: PDB / ID: 4bs3
TitleBovin insulin structure determined by in situ crystal analysis and sulfur-SAD phasing at room temperature
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / MICROPLATE / IN SITU
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 growth hormone / feeding behavior / 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
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsPinker, F. / Stirnimann, C. / Sauter, C. / Olieric, V.
CitationJournal: J.Cryst.Growth / Year: 2013
Title: Chipx: A Novel Microfluidic Chip for Counter- Diffusion Crystallization of Biomolecules and in Situ Crystal Analysis at Room Temperature
Authors: Pinker, F. / Brun, M. / Morin, P. / Deman, A.-L. / Chateau, J.-F. / Olieric, V. / Stirnimann, C. / Lorber, B. / Terrier, N. / Ferrigno, R. / Sauter, C.
History
DepositionJun 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)5,7742
Polymers5,7742
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-14.1 kcal/mol
Surface area3380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.980, 78.980, 78.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

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Components

#1: Protein/peptide INSULIN A CHAIN


Mass: 2369.671 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / References: UniProt: P01317
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 65.9 % / Description: IN SITU SULFUR-SAD AT ROOM TEMPERATURE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.2
Details: INSULIN (30 MG/ML) WAS CRYSTALLIZED AT 293K BY VAPOR DIFFUSION (SITTING DROP) IN CRYSTALQUICK X MICROPLATE USING A RESERVOIR SOLUTION CONTAINING 0.275 M NAHPO4 / NA3PO4 PH 10.2, 0.01 M NA3EDTA.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.7
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.3→55 Å / Num. obs: 3780 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.1
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 14.9 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.301→32.243 Å / SU ML: 0.21 / σ(F): 2.03 / Phase error: 17.62 / Stereochemistry target values: ML
Details: STRUCTURE DETERMINED BY SULFUR SAD PHASING WITH DATA COLLECTED IN SITU AT ROOM TEMPERATURE
RfactorNum. reflection% reflection
Rfree0.1691 353 5.1 %
Rwork0.1561 --
obs0.1568 3681 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.01 Å2
Refinement stepCycle: LAST / Resolution: 2.301→32.243 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms402 0 0 15 417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003413
X-RAY DIFFRACTIONf_angle_d0.589555
X-RAY DIFFRACTIONf_dihedral_angle_d14.897142
X-RAY DIFFRACTIONf_chiral_restr0.05261
X-RAY DIFFRACTIONf_plane_restr0.00272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3011-2.6340.2051100.182129X-RAY DIFFRACTION94
2.634-3.3180.20831220.17712199X-RAY DIFFRACTION100
3.318-32.24660.13941210.13782225X-RAY DIFFRACTION99

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