1SAQ

Crystal Structure of the RNA octamer GIC(GA)GCC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 60: 829-835

  • DOI: 10.1107/S0907444904003804
  • Primary Citation of Related Structures:  

  • 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 mispa ...

    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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'A,B,C,D,E8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.238 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 69.650α = 90.00
b = 69.650β = 90.00
c = 67.810γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance