4INS

THE STRUCTURE OF 2ZN PIG INSULIN CRYSTALS AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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.Hubbard, R.E.Isaacs, N.W.Reynolds, C.D.Sakabe, K.Sakabe, N.Vijayan, N.M.

(1988) Philos Trans R Soc London,ser B 319: 369-456

  • DOI: 10.1098/rstb.1988.0058
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The paper describes the arrangement of the atoms within rhombohedral crystals of 2Zn pig insulin as seen in electron density maps calculated from X-ray data extending to 1.5 A (1 A = 10(-10) m = 10(-1) nm) at room temperature and refined to R = 0.153 ...

    The paper describes the arrangement of the atoms within rhombohedral crystals of 2Zn pig insulin as seen in electron density maps calculated from X-ray data extending to 1.5 A (1 A = 10(-10) m = 10(-1) nm) at room temperature and refined to R = 0.153. The unit cell contains 2 zinc ions, 6 insulin molecules and about 3 x 283 water molecules. The atoms in the protein molecules appear well defined, 7 of the 102 side chains in the asymmetric unit have been assigned alternative disordered positions. The electron density over the water molecules has been interpreted in terms of 349 sites, 217 weighted 1.0, 126 weighted 0.5, 5 at 0.33 and 1 at 0.25 giving ca. 282 molecules. The positions and contacts of all the residues belonging to the two A and B chains of the asymmetric unit are shown first and then details of their arrangement in the two insulin molecules, 1 and 2, which are different. The formation from these molecules of a compact dimer and the further aggregation of three dimers to form a hexamer around two zinc ions, follows. It appears that in the packing of the hexamers in the crystal there are conflicting influences; too-close contacts between histidine B5 residues in neighbouring hexamers are probably responsible for movements of atoms at the beginning of the A chain of one of the two molecules of the dimer that initiate movements in other parts, particularly near the end of the B chain. At every stage of the building of the protein structure, residues to chains of definite conformation, molecules, dimers, hexamers and crystals, we can trace the effect of the packing of like groups to like, aliphatic groups together, aromatic groups together, hydrogen-bonded structures, positive and negative ions. Between the protein molecules, the water is distributed in cavities and channels that are continuous throughout the crystals. More than half the water molecules appear directly hydrogen bonded to protein atoms. These are generally in contact with other water molecules in chains and rings of increasing disorder, corresponding with their movement through the crystals. Within the established crystal structure we survey next the distribution of hydrogen bonds within the protein molecules and between water and protein and water and water; all but eight of the active atoms in the protein form at least one hydrogen bond.(ABSTRACT TRUNCATED AT 400 WORDS)


    Related Citations: 
    • A Comparative Assessment of the Zinc-Protein Coordination in 2Zn-Insulin as Determined by X-Ray Absorption Fine Structure (Exafs) and X-Ray Crystallography
      Bordas, J., Dodson, G.G., Grewe, H., Koch, M.H.J., Krebs, B., Randall, J.
      (1983) Proc R Soc London,ser B 219: 21
    • Structural Relationships in the Two-Zinc Insulin Hexamer
      Dodson, E.J., Dodson, G.G., Hodgkin, D.C., Reynolds, C.D.
      (1979) Can J Biochem 57: 469
    • Experience with Fast Fourier Least Squares in the Refinement of the Crystal Structure of Rhombohedral 2-Zinc Insulin at 1.5 Angstroms Resolution
      Isaacs, N.W., Agarwal, R.C.
      (1978) Acta Crystallogr A 34: 782
    • Rhombohedral Insulin Crystal Transformation
      Bentley, G., Dodson, G., Lewitova, A.
      (1978) J Mol Biol 126: 871
    • A Method for Fitting Satisfactory Models to Sets of Atomic Positions in Protein Structure Refinements
      Dodson, E.J., Isaacs, N.W., Rollett, J.S.
      (1976) Acta Crystallogr A 32: 311
    • Varieties of Insulin
      Hodgkin, D.C.
      (1974) J Endocrinol 63: 1
    • The Structure of Insulin
      Hodgkin, D.C.
      (1972) Dan Tidsskr Farm 46: 1
    • Insulin. The Structure in the Crystal and its Reflection in Chemistry and Biology
      Blundell, T., Dodson, G., Hodgkin, D., Mercola, D.
      (1972) Adv Protein Chem 26: 279
    • The Crystal Structure of Rhombohedral 2 Zinc Insulin
      Blundell, T.L., Cutfield, J.F., Dodson, E.J., Dodson, G.G., Hodgkin, D.C., Mercola, D.A.
      (1972) Cold Spring Harb Symp Quant Biol 36: 233
    • Atomic Positions in Rhombohedral 2-Zinc Insulin Crystals
      Blundell, T.L., Cutfield, J.F., Cutfield, S.M., Dodson, E.J., Dodson, G.G., Hodgkin, D.C., Mercola, D.A., Vijayan, M.
      (1971) Nature 231: 506
    • X-Ray Analysis and the Structure of Insulin
      Blundell, T.L., Dodson, G.G., Dodson, E., Hodgkin, D.C., Vijayan, M.
      (1971) Recent Prog Horm Res 27: 1
    • X-Ray Diffraction Data on Some Crystalline Varieties of Insulin
      Baker, E.N., Dodson, G.
      (1970) J Mol Biol 54: 605
    • Structure of Rhombohedral 2 Zinc Insulin Crystals
      Adams, M.J., Blundell, T.L., Dodson, E.J., Dodson, G.G., Vijayan, M., Baker, E.N., Harding, M.M., Hodgkin, D.C., Rimmer, B., Sheat, S.
      (1969) Nature 224: 491

    Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INSULIN (CHAIN A)
A, C
21Sus scrofaMutation(s): 0 
Gene Names: INS
Find proteins for P01315 (Sus scrofa)
Go to UniProtKB:  P01315

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INSULIN (CHAIN B)
B, D
30Sus scrofaMutation(s): 0 
Gene Names: INS
Find proteins for P01315 (Sus scrofa)
Go to UniProtKB:  P01315
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.153 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.5α = 90
b = 82.5β = 90
c = 34γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-04-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-02-29
    Changes: Database references
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other