4M4M

The structure of Ni T6 bovine insulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6 bovine insulin derivatives.

Frankaer, C.G.Mossin, S.Stahl, K.Harris, P.

(2014) Acta Crystallogr.,Sect.D 70: 110-122

  • DOI: 10.1107/S1399004713029040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using synchrotron radiation (SR), the crystal structures of T6 bovine insulin complexed with Ni(2+) and Cu(2+) were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limite ...

    Using synchrotron radiation (SR), the crystal structures of T6 bovine insulin complexed with Ni(2+) and Cu(2+) were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni(2+) with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu(2+) as a result of the Jahn-Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu(2+) is sensitive towards photoreduction when exposed to SR. During the reduction of Cu(2+) to Cu(+), the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent radiation damage was carried out by solid embedment of Cu insulin in a saccharose matrix. At 100 K the photoreduction was suppressed by ∼15%, and it was suppressed by a further ∼30% on cooling the samples to 20 K.


    Organizational Affiliation

    Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kgs. Lyngby, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin
A, C
21Bos taurusMutation(s): 0 
Gene Names: INS
Find proteins for P01317 (Bos taurus)
Go to Gene View: INS
Go to UniProtKB:  P01317
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Insulin
B, D
30Bos taurusMutation(s): 0 
Gene Names: INS
Find proteins for P01317 (Bos taurus)
Go to Gene View: INS
Go to UniProtKB:  P01317
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
B, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.182 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 80.850α = 90.00
b = 80.850β = 90.00
c = 33.360γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MAR345dtbdata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-12
    Type: Database references
  • Version 1.2: 2018-03-07
    Type: Data collection