4X4B

RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (DWD) 2.1 MGy


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Radiation damage to nucleoprotein complexes in macromolecular crystallography.

Bury, C.Garman, E.F.Ginn, H.M.Ravelli, R.B.Carmichael, I.Kneale, G.McGeehan, J.E.

(2015) J Synchrotron Radiat 22: 213-224

  • DOI: 10.1107/S1600577514026289
  • Primary Citation of Related Structures:  
    4X4H, 4X4I, 4X4B, 4X4C, 4X4D, 4X4E, 4X4F, 4X4G

  • PubMed Abstract: 
  • Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the lar ...

    Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.


    Related Citations: 
    • Structural analysis of the genetic switch that regulates the expression of restriction-modification genes
      McGeehan, J.E., Streeter, S.D., Thresh, S.J., Ball, N., Ravelli, R.B.G., Kneale, G.G.
      (2008) Nucleic Acids Res 36: 4778

    Organizational Affiliation

    Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory proteinABCD82Enterobacter sp. RFL1396Mutation(s): 0 
Gene Names: esp1396IC
Find proteins for Q8GGH0 (Enterobacter sp. RFL1396)
Explore Q8GGH0 
Go to UniProtKB:  Q8GGH0
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
35-MER DNAE35synthetic construct
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
35-MER DNAF35synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.31α = 90
b = 104.31β = 90
c = 139.13γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations