1SAQ

Crystal Structure of the RNA octamer GIC(GA)GCC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structures of two RNA octamers containing tandem G.A base pairs.

Jang, S.B.Baeyens, K.Jeong, M.S.SantaLucia, J.Turner, D.Holbrook, S.R.

(2004) Acta Crystallogr D Biol Crystallogr 60: 829-835

  • DOI: https://doi.org/10.1107/S0907444904003804
  • Primary Citation of Related Structures:  
    1SA9, 1SAQ

  • PubMed Abstract: 

    The crystal structures of two RNA octamers, 5'-GGC(GA)GCC-3' and 5'-GIC(GA)GCC-3', have been determined from X-ray diffraction data to 2.8 and 2.7 A resolution, respectively. The RNA octamers crystallize in isomorphous unit cells containing two mispairs arranged in a self-complementary manner and one single strand in the asymmetric unit. The single strand pairs with another single strand related by crystallographic symmetry to form a third unique double helix. Tandem non-Watson-Crick G.A/A.G base pairs of the sheared type comprise an internal loop in the middle of each duplex. The NMR structure of this octameric RNA sequence is also known, allowing comparison of the variation between the six crystallographic duplexes and the solution structure. In the symmetric duplex of the octamer containing inosine, the sheared G.A pairs incorporate a bound water molecule. This duplex also binds one water molecule per strand in the minor groove adjacent to the G.A pairs.


  • Organizational Affiliation

    Korea Nanobiotechnology Center, Pusan National University, Busan 609-735, South Korea. sbjang@pusan.ac.kr


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'
A, B, C, D, E
8N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.65α = 90
b = 69.65β = 90
c = 67.81γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references