1QBP

CRYSTAL STRUCTURE OF A BROMINATED RNA HELIX WITH FOUR MISMATCHED BASE PAIRS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a brominated RNA helix with four mismatched base pairs: An investigation into RNA conformational variability.

Anderson, A.C.O'Neil, R.H.Filman, D.J.Frederick, C.A.

(1999) Biochemistry 38: 12577-12585


  • PubMed Abstract: 
  • The X-ray crystal structure of a brominated RNA helix with four mismatched base pairs and sequence r(UG(Br)C(Br)CAGUUCGCUGGC)(2) was determined to 2.1 A using the methods of multiwavelength anomalous diffraction (MAD) applied to the bromine K-absorpt ...

    The X-ray crystal structure of a brominated RNA helix with four mismatched base pairs and sequence r(UG(Br)C(Br)CAGUUCGCUGGC)(2) was determined to 2.1 A using the methods of multiwavelength anomalous diffraction (MAD) applied to the bromine K-absorption edge. There are three molecules in the asymmetric unit with unique crystal-packing environments, revealing true conformational variability at high resolution for this sequence. The structure shows that the sequence itself does not define a consistent pattern of solvent molecules, with the exception of the mismatched base pairs, implying that specific RNA-protein interactions would occur only with the nucleotides. There are a number of significant tertiary interactions, some of which are a result of the brominated base pairs and others that are directly mediated by the RNA 2' hydroxyl groups. The mismatched base pairs exhibit a solvent network as well as a stacking pattern with their nearest neighbors that validate previous thermodynamic analysis.


    Organizational Affiliation

    Committee on Biophysics, Harvard University and Dana-Farber Cancer Institute, 44 Binney Street, S1036, Boston, Massachusetts 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3'A,B,C,D,E,F15N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBV
Query on CBV
A, B, C, D, E, F
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.450α = 90.00
b = 24.270β = 118.76
c = 104.450γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
TRUNCATEdata reduction
CCP4data scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance