402D

5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3'


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an RNA internal loop consisting of tandem C-A+ base pairs.

Jang, S.B.Hung, L.W.Chi, Y.I.Holbrook, E.L.Carter, R.J.Holbrook, S.R.

(1998) Biochemistry 37: 11726-11731

  • DOI: 10.1021/bi980758j

  • PubMed Abstract: 
  • The crystal structure of the RNA octamer 5'-CGC(CA)GCG-3' has been determined from X-ray diffraction data to 2.3 A resolution. In the crystal, this oligomer forms a self-complementary double helix in the asymmetric unit. Tandem non-Watson-Crick C-A a ...

    The crystal structure of the RNA octamer 5'-CGC(CA)GCG-3' has been determined from X-ray diffraction data to 2.3 A resolution. In the crystal, this oligomer forms a self-complementary double helix in the asymmetric unit. Tandem non-Watson-Crick C-A and A-C base pairs comprise an internal loop in the middle of the duplex, which is incorporated with little distortion of the A-form double helix. From the geometry of the C-A base pairs, it is inferred that the adenosine imino group is protonated and donates a hydrogen bond to the carbonyl group of the cytosine. The wobble geometry of the C-A+ base pairs is very similar to that of the common U-G non-Watson-Crick pair.


    Organizational Affiliation

    Structural Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA(5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3')A,B8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 42.737α = 90.00
b = 42.737β = 90.00
c = 123.900γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-16
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance