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- PDB-5azz: Crystal structure of seleno-insulin -

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Basic information

Entry
Database: PDB / ID: 5azz
TitleCrystal structure of seleno-insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / selenocysteine / insulin
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 / SAD / Resolution: 1.45 Å
AuthorsWatanabe, S. / Okumura, M. / Arai, K. / Takei, T. / Asahina, Y. / Hojo, H. / Iwaoka, M. / Inaba, K.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Preparation of Selenoinsulin as a Long-Lasting Insulin Analogue.
Authors: Arai, K. / Takei, T. / Okumura, M. / Watanabe, S. / Amagai, Y. / Asahina, Y. / Moroder, L. / Hojo, H. / Inaba, K. / Iwaoka, M.
History
DepositionOct 23, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last

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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)6,1002
Polymers6,1002
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area3210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.994, 77.994, 77.994
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-119-

HOH

21B-124-

HOH

31B-138-

HOH

41B-141-

HOH

51B-143-

HOH

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Components

#1: Protein/peptide Insulin A chain


Mass: 2517.736 Da / Num. of mol.: 1 / Mutation: C7(SEC) / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P01317
#2: Protein/peptide Insulin B chain


Mass: 3582.018 Da / Num. of mol.: 1 / Mutation: C7(SEC) / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P01317
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.05 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: Sodium chloride, ethylene imine polymer, citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.45→39 Å / Num. obs: 27239 / % possible obs: 100 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 11.4
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 11 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→39 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 19.94 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1916 1454 5.34 %
Rwork0.1683 --
obs0.1696 27238 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms389 0 0 74 463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017447
X-RAY DIFFRACTIONf_angle_d1.063616
X-RAY DIFFRACTIONf_dihedral_angle_d22.058156
X-RAY DIFFRACTIONf_chiral_restr0.07867
X-RAY DIFFRACTIONf_plane_restr0.00383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4493-1.50110.25191380.23362610X-RAY DIFFRACTION100
1.5011-1.56120.22961360.21652586X-RAY DIFFRACTION100
1.5612-1.63230.19161200.1992573X-RAY DIFFRACTION100
1.6323-1.71830.21971560.18782560X-RAY DIFFRACTION100
1.7183-1.8260.19221540.18212609X-RAY DIFFRACTION100
1.826-1.9670.22721440.17812556X-RAY DIFFRACTION100
1.967-2.16490.19851280.16312610X-RAY DIFFRACTION100
2.1649-2.47810.18831820.16462502X-RAY DIFFRACTION100
2.4781-3.1220.18461380.16332614X-RAY DIFFRACTION100
3.122-39.01110.17551580.152564X-RAY DIFFRACTION100

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