1R41

Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.

Shi, K.Pan, B.Tippin, D.Sundaralingam, M.

(2004) Acta Crystallogr.,Sect.D 60: 61-65

  • Primary Citation of Related Structures:  1R3Z

  • PubMed Abstract: 
  • The crystal structures of two alternating octamers d(Gm(5)CGm(5)CGCGC) and d(GCGCGm(5)CGm(5)C) have been determined at 1.7 and 1.9 A resolution with R(work)/R(free) of 16.9/19.6% and 17.9/19.8%, respectively. The two octamers crystallized in the same ...

    The crystal structures of two alternating octamers d(Gm(5)CGm(5)CGCGC) and d(GCGCGm(5)CGm(5)C) have been determined at 1.7 and 1.9 A resolution with R(work)/R(free) of 16.9/19.6% and 17.9/19.8%, respectively. The two octamers crystallized in the same tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 43.0, c = 24.9 A and a = b = 43.1, c = 24.7 A, respectively. Both structures adopt the A-type double helix and the abutting crystal packing. Despite the different positions of the methylated cytosine in the sequence, the two octamers display essentially the same conformation. The close similarity of the two structures indicates that methylation at different positions in a DNA sequence does not affect the helical conformation of the alternating DNA octamer. Investigation of other related crystal structures implies that methylation of cytosine stabilizes the A-type conformation for alternating DNA sequences beginning with a 5'-purine but is beneficial to the Z-type conformation for alternating DNA sequences beginning with a 5'-pyrimidine.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'A8N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
A
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 43.120α = 90.00
b = 43.120β = 90.00
c = 24.770γ = 90.00

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance