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- PDB-1izb: ROLE OF B13 GLU IN INSULIN ASSEMBLY: THE HEXAMER STRUCTURE OF REC... -

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Basic information

Entry
Database: PDB / ID: 1izb
TitleROLE OF B13 GLU IN INSULIN ASSEMBLY: THE HEXAMER STRUCTURE OF RECOMBINANT MUTANT (B13 GLU-> GLN) INSULIN
Components(INSULIN) x 2
KeywordsHORMONE
Function / homology
Function and homology information


glycoprotein biosynthetic process / lactate biosynthetic process / positive regulation of lipoprotein lipase activity / positive regulation of fatty acid biosynthetic process / response to L-arginine / lipoprotein biosynthetic process / positive regulation of glucose metabolic process / lipid biosynthetic process / alpha-beta T cell activation / negative regulation of glycogen catabolic process ...glycoprotein biosynthetic process / lactate biosynthetic process / positive regulation of lipoprotein lipase activity / positive regulation of fatty acid biosynthetic process / response to L-arginine / lipoprotein biosynthetic process / positive regulation of glucose metabolic process / lipid biosynthetic process / alpha-beta T cell activation / negative regulation of glycogen catabolic process / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / negative regulation of reactive oxygen species biosynthetic process / regulation of cellular amino acid metabolic process / regulation of protein localization to plasma membrane / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of protein secretion / negative regulation of lipid catabolic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of DNA replication / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / positive regulation of mitotic nuclear division / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / glucose homeostasis / wound healing / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like / Insulin-like superfamily / Insulin, conserved site / Insulin family signature.
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsXiao, B. / Dodson, G.G.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Role of B13 Glu in insulin assembly. The hexamer structure of recombinant mutant (B13 Glu-->Gln) insulin.
Authors: Bentley, G.A. / Brange, J. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Markussen, J. / Wilkinson, A.J. / Wollmer, A. / Xiao, B.
History
DepositionOct 16, 1992-
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7646
Polymers11,6334
Non-polymers1312
Water2,252125
1
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8823
Polymers5,8172
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-15 kcal/mol
Surface area3700 Å2
MethodPISA
2
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8823
Polymers5,8172
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-16 kcal/mol
Surface area3570 Å2
MethodPISA
3
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,29218
Polymers34,90012
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20100 Å2
ΔGint-252 kcal/mol
Surface area12070 Å2
MethodPISA
4
A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,29218
Polymers34,90012
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-y,x-y,z+11
crystal symmetry operation3_556-x+y,-x,z+11
Buried area13590 Å2
ΔGint-198 kcal/mol
Surface area18580 Å2
MethodPISA
5
A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6469
Polymers17,4506
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5430 Å2
ΔGint-96 kcal/mol
Surface area10660 Å2
MethodPISA
6
C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6469
Polymers17,4506
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5770 Å2
ΔGint-94 kcal/mol
Surface area10320 Å2
MethodPISA
7
A: INSULIN
B: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7646
Polymers11,6334
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4990 Å2
ΔGint-44 kcal/mol
Surface area5670 Å2
MethodPISA
8


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-38 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)82.850, 82.850, 34.100
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-102-

ZN

31B-110-

HOH

41B-121-

HOH

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Components

#1: Protein/peptide INSULIN /


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide INSULIN /


Mass: 3432.968 Da / Num. of mol.: 2 / Mutation: E13Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.94 Å3/Da / Density % sol: 36.46 %
Crystal grow
*PLUS
pH: 6.2 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.02 M11HCl
22 mg/mlzinc acetate11
350 mMNa3 citrate11
416 %(v/v)acetone11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 5369 / % possible obs: 91.1 % / Rmerge(I) obs: 0.05

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.18 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 2 125 937
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection obs: 5369 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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