1L3Z

Crystal Structure Analysis of an RNA Heptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs

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

(2003) Nucleic Acids Res 31: 1392-1397

  • DOI: 10.1093/nar/gkg226
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of an alternating RNA heptamer r(GUAUACA) has been determined to 2.0 A resolution and refined to an R(work) of 17.1% and R(free) of 18.5% using 2797 reflections. The heptamer crystallized in the space group C222 with a unit cell ...

    The crystal structure of an alternating RNA heptamer r(GUAUACA) has been determined to 2.0 A resolution and refined to an R(work) of 17.1% and R(free) of 18.5% using 2797 reflections. The heptamer crystallized in the space group C222 with a unit cell of a = 25.74, b = 106.58, c = 30.26 A and two independent strands in the asymmetric unit. Each heptamer forms a duplex with its symmetry-related strand and each duplex contains six Watson-Crick base pairs and 3'-end adenosine overhangs. Therefore, two kinds of duplex (duplex 1 and duplex 2) are formed. Duplexes 1 stack on each other forming a pseudo-continuous column, which is typical of the RNA packing mode, while duplex 2 is typical of A-DNA packing with its termini in abutting interactions. Overhang adenine residues stack within the duplexes with C3'-endo sugar pucker and C2'-endo sugar pucker in duplexes 1 and 2, respectively. A Na+ ion in the crystal lattice is water bridged to two N1 atoms of symmetry-related A7 bases.


    Organizational Affiliation

    Department of Chemistry, The Ohio State University, 200 Johnston Laboratory, Columbus, OH 43210, USA.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*UP*AP*UP*AP*CP*A)-3'A, B7N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.74α = 90
b = 106.58β = 90
c = 30.26γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-03-07
    Changes: Data collection