1EVP

CRYSTAL STRUCTURE OF THE CHIMERICAL DECAMER D(CCACTAGTG)R(G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G).

Wahl, M.C.Sundaralingam, M.

(2000) Nucleic Acids Res. 28: 4356-4363


  • PubMed Abstract: 
  • The crystal structure of the chimerical decamer d(CCACTAGTG)r(G), bearing a 3'-terminal ribo-guanidine, has been solved and refined at 1.8 A resolution (R-factor 16.6%; free R-factor 22.8%). The decamer crystallizes in the orthorhombic space group P2 ...

    The crystal structure of the chimerical decamer d(CCACTAGTG)r(G), bearing a 3'-terminal ribo-guanidine, has been solved and refined at 1.8 A resolution (R-factor 16.6%; free R-factor 22.8%). The decamer crystallizes in the orthorhombic space group P2(1)2(1)2(1) with unit cell constants a = 23.90 A, b = 45.76 A and c = 49.27 A. The structure was solved by molecular replacement using the coordinates of the isomorphous chimera r(GCG)d(TATACGC). The final model contains one duplex and 77 water molecules per asymmetric unit. Surprisingly, all residues adopt a conformation typical for A-form nucleic acids (C3'-endo type sugar pucker) although the all-DNA analog, d(CCACTAGTGG), has been crystallized in the B-form. Comparing circular dichroism spectra of the chimera and the corresponding all-DNA sequence reveals a similar trend of the former molecule to adopt an A-like conformation in solution. The results suggest that the preference of ribonucleotides for the A-form is communicated into the 5'-direction of an oligonucleotide strand, although direct interactions of the 2'-hydroxyl group can only be discerned with nucleotides in the 3'-direction of a C3'-endo puckered ribose. These observations imply that forces like water-mediated contacts, the concerted motions of backbone torsion angles, and stacking preferences, are responsible for such long-range influences. This bi-directional structural communication originating from a ribonucleotide can be expected to contribute to the stability of the A-form within all-RNA duplexes.


    Organizational Affiliation

    The Ohio State University, Laboratory of Biological Macromolecular Structure, Departments of Chemistry, Biochemistry, and the Ohio State Biochemistry Program, 012 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210-1002, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(*CP*CP*AP*CP*TP*AP*GP*TP*GP)-R(*G)-3')Q,R10N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 23.900α = 90.00
b = 45.760β = 90.00
c = 49.270γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-GENdata scaling
X-GENdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description