455D

A6/A18 INTER-STRAND DITHIOBIS(PROPANE)-CROSSLINKED DODECAMER (CGCGAATTCGCG)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G.

Chiu, T.K.Kaczor-Grzeskowiak, M.Dickerson, R.E.

(1999) J.Mol.Biol. 292: 589-608

  • DOI: 10.1006/jmbi.1999.3075

  • PubMed Abstract: 
  • The structure of a crosslinked B -DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved to a resolution of 1.43 A. The dithiobis-propane crosslink, -CH2-CH2-CH2-S-S-CH2-CH2-CH2-, bridges N7 atoms of adenine bases 6 and 18 in the two centr ...

    The structure of a crosslinked B -DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved to a resolution of 1.43 A. The dithiobis-propane crosslink, -CH2-CH2-CH2-S-S-CH2-CH2-CH2-, bridges N7 atoms of adenine bases 6 and 18 in the two central base-pairs within the major groove. The crosslink is sufficiently long that no bending is induced in the helix, which is essentially isostructural with the native unlinked dodecamer at 1.9 A. A constellation of solvent peaks tentatively fitted as a spermine molecule in that earlier analysis is now seen at higher resolution to be a well-defined octahedral magnesium hexahydrate complex in the major groove. One end of the duplex curves around that complex to produce a roll-bend near base-pairs 3-5, and an overall bend in helix axis, as has long been noted. Two other magnesium complexes connect the helices and help to knit the crystal lattice together. No evidence exists for partial sodium or potassium ion substitution for solvent water molecules within the minor groove spine of hydration, as had been suggested previously: not coordination geometry and environment, nor B values, nor calculated valence values, nor difference map analyses. Indeed, the very numbers that have been claimed in support of partial substitution by sodium or potassium ions are reproduced with the present crystals, which by chemical analysis contains only one trace sodium ion per 160 bp, and one potassium ion per 41 bp. In contrast, our crystals contain one Mg2+ per base-pair, meaning that phosphate group charge neutrality is accomplished by divalent cations, not monovalent ions. Three of these magnesium cations per duplex are localized and visible in the X-ray analysis, and nine are disordered and invisible. Hence although binding of monovalent cations within the minor groove of A -tracts on occasion may be a consequence of groove narrowing, it cannot be the cause of that narrowing. Cations, contrary to what has been claimed, are not in charge.


    Organizational Affiliation

    Molecular Biology Institute and the Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*(SSP)AP*TP*TP*CP*GP*CP*G)-3')A,B12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSP
Query on SSP

Download SDF File 
Download CCD File 
A
DITHIOBIS-(PROPANE)
C6 H14 S2
ALVPFGSHPUPROW-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 24.544α = 90.00
b = 39.303β = 90.00
c = 66.964γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-10-08
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance