3FHP

A neutron crystallographic analysis of a porcine 2Zn insulin at 2.0 A resolution

Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

A neutron crystallographic analysis of T6 porcine insulin at 2.1 A resolution

Iwai, W., Yamada, T., Kurihara, K., Ohnishi, Y., Kobayashi, Y., Tanaka, I., Takahashi, H., Kuroki, R., Tamada, T., Niimura, N.

(2009) Acta Crystallogr.,Sect.D 65: 1042-1050

  • DOI: 10.1107/S090744490902770X

  • PubMed Abstract: 

    • Neutron diffraction data for T(6) porcine insulin were collected to 2.1 A resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structu ...

    Neutron diffraction data for T(6) porcine insulin were collected to 2.1 A resolution from a single crystal partly deuterated by exchange of mother liquor. A maximum-likelihood structure refinement was undertaken using the neutron data and the structure was refined to a residual of 0.179. The hydrogen-bonding network of the central core of the hexamer was observed and the charge balance between positively charged Zn ions and their surrounding structure was interpreted by considering the protonation and/or deprotonation states and interactions of HisB10, water and GluB13. The observed double conformation of GluB13 was essential to interpreting the charge balance and could be compared with the structure of a dried crystal of T(6) human insulin at 100 K. Differences in the dynamic behaviour of the water molecules coordinating the upper and lower Zn ions were observed and interpreted. The hydrogen bonds in the insulin molecules, as well as those involving HisB10 and GluB13, are discussed. The hydrogen/deuterium (H/D) exchange ratios of the amide H atoms of T(6) porcine insulin in crystals were obtained and showed that regions highly protected from H/D exchange are concentrated in the centre of a helical region of the B chains. From the viewpoint of soaking time versus H/D-exchange ratios, the amide H atoms can be classified into three categories.

    Organizational Affiliation: 

    Graduate School of Science and Engineering, Ibaraki University, Hitachi, Ibaraki 316-8511, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin
A, C
21Sus scrofaMutation(s): 0 
Gene Names: INS
Find proteins for P01315 (Sus scrofa)
Go to Gene View: INS
Go to UniProtKB:  P01315
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Insulin
B, D
30Sus scrofaMutation(s): 0 
Gene Names: INS
Find proteins for P01315 (Sus scrofa)
Go to Gene View: INS
Go to UniProtKB:  P01315
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
B, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DOD
Query on DOD
Download SDF File 
Download CCD File 
A, B, C, D
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.168 
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
CNSphasing
XFITdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2013-08-21
    Type: Other
  • Version 1.3: 2018-03-07
    Type: Data collection
  • Version 1.4: 2018-06-13
    Type: Data collection
  • Version 1.5: 2018-07-18
    Type: Data collection