4C5X

Ultra High Resolution Dickerson-Drew dodecamer B-DNA with 5-Hydroxymethyl-cytosine Modification


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights Into How 5-Hydroxymethylation Influences Transcription Factor Binding.

Lercher, L.Mcdonough, M.A.El-Sagheer, A.H.Thalhammer, A.Kriaucionis, S.Brown, T.Schofield, C.J.

(2014) Chem.Commun.(Camb.) 50: 1794

  • DOI: 10.1039/c3cc48151d
  • Primary Citation of Related Structures:  4C63, 4C64

  • PubMed Abstract: 
  • Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription b ...

    Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor interactions.


    Organizational Affiliation

    Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, Oxford, UK. Christopher.schofield@chem.ox.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(CP*GP*CP*GP*AP*AP*TP*TP*5HCP*GP*CP*GP)-3'A,B12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5HC
Query on 5HC
A, B
DNA LINKINGC10 H16 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.300α = 90.00
b = 40.270β = 90.00
c = 64.880γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Database references