1OS3

Dehydrated T6 human insulin at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Lessons from an aged, dried crystal of T(6) human insulin.

Smith, G.D.Blessing, R.H.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1384-1394

  • DOI: 10.1107/s090744490301165x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of the T(6) hexameric form of human insulin has been determined at both room temperature and 100 K from a single air-dried crystal. At 100 K, the space group is R3 and the asymmetric unit consists of a dimer, as has been observed previo ...

    The structure of the T(6) hexameric form of human insulin has been determined at both room temperature and 100 K from a single air-dried crystal. At 100 K, the space group is R3 and the asymmetric unit consists of a dimer, as has been observed previously in hydrated structures. At room temperature, the space group is P1 and the unit cell contains a quasi-threefold-symmetric hexamer. In the absence of stabilizing water interactions, the N-termini of all six A chains in the room-temperature structure appear to have undergone partial unfolding, but the N-termini of these chains are well ordered in the 100 K structure. Other differences between the room-temperature and 100 K structures involve the coordination around the zinc ions. At 100 K, both zinc ions clearly exhibit dual coordination: zinc is octahedrally coordinated in one half of the zinc sites but tetrahedrally coordinated in the other half; at room temperature, the electron densities suggest tetrahedral coordination but the bond distances to the fourth ligands are longer than expected. Contrary to what has been observed to date in all other T(6) insulin structures, there are no contacts between pairs of GluB13 residues, either at room temperature or at 100 K, that would suggest the presence of a hydrogen bond. At room temperature, three of the six independent GluB13 side chains are disordered; at 100 K, both independent side chains are disordered. The disorder in the GluB13 side chains and the lack of contacts between carboxylate groups suggests that as a result of disruption of the hydration structure in the central core of the hexamer, all six B13 carboxylates bear a negative charge. This in turn suggests that in the hydrated structures the well ordered water structure in the central core is involved in stabilizing the B13 side-chain conformations and modulating charge repulsions among the six B13 glutamates if they are not protonated, or that, as is considered more likely, the water structure plays an important role in modulating the pK(a) values of the B13 glutamates, resulting in protonation and hydrogen-bond formation.


    Related Citations: 
    • The structure of T6 human insulin at 1.0 A resolution.
      Smith, G.D., Pangborn, W.A., Blessing, R.H.
      (2003) Acta Crystallogr D Biol Crystallogr 59: 474
    • The structure of 2Zn pig insulin crystals at 1.5 A resolution
      Baker, E.N., Blundell, T.L., Cutfield, J.F., Cutfield, S.M., Dodson, E.J., Dodson, G.G., Hodgkin, D.M.C., Hubbard, R.E., Isaacs, N.W., Reynolds, C.D.
      (1988) Philos Trans R Soc London,ser B 319: 369
    • Structure of insulin: Results of joint neutron and X-ray refinement.
      Wlodawer, A., Savage, H., Dodson, G.
      (1989) Acta Crystallogr B 45: 99

    Organizational Affiliation

    Structural Biology and Biochemistry, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada. gdsmith@sauron.psf.sickkids.on.ca



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
InsulinA, C21Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS  P01308
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
InsulinB, D30Homo sapiensMutation(s): 0 
Gene Names: INS
Find proteins for P01308 (Homo sapiens)
Explore P01308 
Go to UniProtKB:  P01308
NIH Common Fund Data Resources
PHAROS  P01308
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.216 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.51α = 90
b = 81.51β = 90
c = 33.76γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance