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- PDB-4e7u: The structure of T3R3 bovine insulin -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4e7u
TitleThe structure of T3R3 bovine insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Zinc binding
Function / homology
Function and homology information


positive regulation of blood circulation / estradiol secretion / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of lactation / positive regulation of cell maturation / response to L-arginine / response to butyrate / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite ...positive regulation of blood circulation / estradiol secretion / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of lactation / positive regulation of cell maturation / response to L-arginine / response to butyrate / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / feeding behavior / response to food / positive regulation of Rho protein signal transduction / response to growth hormone / positive regulation of peptide hormone secretion / positive regulation of insulin secretion / protein secretion / negative regulation of lipid catabolic process / response to glucose / response to nutrient levels / positive regulation of protein secretion / hormone activity / insulin receptor binding / glucose metabolic process / positive regulation of phosphatidylinositol 3-kinase signaling / response to heat / 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-like superfamily / Insulin, conserved site / Insulin family signature.
Similarity search - Domain/homology
THIOCYANATE ION / Insulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHarris, P. / Frankaer, C.G. / Knudsen, M.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: The structures of T(6), T(3)R(3) and R(6) bovine insulin: combining X-ray diffraction and absorption spectroscopy.
Authors: Frankar, C.G. / Knudsen, M.V. / Noren, K. / Nazarenko, E. / Stahl, K. / Harris, P.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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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)11,6767
Polymers11,4874
Non-polymers1893
Water1,76598
1
A: Insulin A chain
B: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8093
Polymers5,7442
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-14 kcal/mol
Surface area3440 Å2
MethodPISA
2
C: Insulin A chain
D: Insulin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8674
Polymers5,7442
Non-polymers1232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-13 kcal/mol
Surface area3630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.200, 79.200, 37.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21D-101-

ZN

31D-102-

SCN

41D-102-

SCN

51D-102-

SCN

61B-222-

HOH

71D-217-

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: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.96 Å3/Da / Density % sol: 37.11 %
Crystal growTemperature: 298 K / Method: batch method / pH: 6.4
Details: 6.5mg/ml bovine insulin, 7mM zinc acetate, 0.05M sodium citrate, 15% acetone, 0.2M KSCN, pH 6.4, BATCH METHOD, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0391 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 28, 2010
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0391 Å / Relative weight: 1
ReflectionResolution: 1.23→21.27 Å / Num. all: 23527 / Num. obs: 23527 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 2010_07_29_2140)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BEN
Resolution: 1.3→21.27 Å / SU ML: 0.16 / σ(F): 2 / Phase error: 14.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 1024 5 %RANDOM
Rwork0.1439 ---
obs0.1457 20467 95.58 %-
all-20467 --
Solvent computationShrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.077 Å2 / ksol: 0.539 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5047 Å2-0 Å20 Å2
2---0.5047 Å20 Å2
3---1.0094 Å2
Refinement stepCycle: LAST / Resolution: 1.3→21.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 5 98 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008822
X-RAY DIFFRACTIONf_angle_d1.0381107
X-RAY DIFFRACTIONf_dihedral_angle_d12.439289
X-RAY DIFFRACTIONf_chiral_restr0.068122
X-RAY DIFFRACTIONf_plane_restr0.005145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.36860.2441530.20842897X-RAY DIFFRACTION100
1.3686-1.45430.19481510.16752878X-RAY DIFFRACTION99
1.4543-1.56660.16751510.12962869X-RAY DIFFRACTION99
1.5666-1.72420.16231510.11732873X-RAY DIFFRACTION99
1.7242-1.97350.1711500.11832838X-RAY DIFFRACTION97
1.9735-2.48580.1631480.12452812X-RAY DIFFRACTION96
2.4858-21.27560.19231200.16742276X-RAY DIFFRACTION79

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