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- PDB-6qq7: Bovine insulin at ambient pressure -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6qq7
TitleBovine insulin at ambient pressure
Components(Insulin) x 2
KeywordsHORMONE / glucose metabolism
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKurpiewska, K. / Milaczewska, A. / Lewinski, K.
CitationJournal: J.Mol.Struct. / Year: 2020
Title: Insulin conformational changes under high pressure in structural studies and molecular dynamics simulations
Authors: Kurpiewska, K. / Milaczewska, A. / Lewinski, K.
History
DepositionFeb 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7442
Polymers5,7442
Non-polymers00
Water50428
1
A: Insulin
B: Insulin

A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)11,4874
Polymers11,4874
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_545-x,-y-1/2,z1
Buried area4330 Å2
ΔGint-37 kcal/mol
Surface area5470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.767, 78.767, 78.767
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-111-

HOH

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Components

#1: Protein/peptide Insulin /


Mass: 2339.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin /


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 / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 0.01 M Na2HPO4, 0.1 M Na2EDTA

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.5418 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Nov 9, 2010
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→15.45 Å / Num. obs: 9941 / % possible obs: 99.97 % / Redundancy: 18.1 % / Biso Wilson estimate: 20.9 Å2 / CC1/2: 1 / Net I/σ(I): 17.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.39 / Num. unique obs: 489 / CC1/2: 0.616 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
CrysalisProdata collection
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BN3

2bn3


Resolution: 1.65→15.447 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.19
RfactorNum. reflection% reflection
Rfree0.1901 980 9.86 %
Rwork0.1728 --
obs0.1746 9941 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→15.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms400 0 0 28 428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007491
X-RAY DIFFRACTIONf_angle_d0.738678
X-RAY DIFFRACTIONf_dihedral_angle_d10.166352
X-RAY DIFFRACTIONf_chiral_restr0.05170
X-RAY DIFFRACTIONf_plane_restr0.00493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6503-1.73720.28381330.27691270X-RAY DIFFRACTION100
1.7372-1.84590.21441390.2331270X-RAY DIFFRACTION100
1.8459-1.98810.241360.21421270X-RAY DIFFRACTION100
1.9881-2.18770.18911390.17741267X-RAY DIFFRACTION100
2.1877-2.50310.20671370.18621263X-RAY DIFFRACTION100
2.5031-3.14930.20741510.18281299X-RAY DIFFRACTION100
3.1493-15.44810.15421450.13381322X-RAY DIFFRACTION100

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