1ET4

CRYSTAL STRUCTURE OF A VITAMIN B12 BINDING RNA APTAMER WITH LIGAND AT 2.3 A

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2000-04-12 Released: 2000-11-13 
  • Deposition Author(s): Sussman, D., Wilson, C.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

A water channel in the core of the vitamin B(12) RNA aptamer.

Sussman, D., Wilson, C.

(2000) Structure 8: 719-727

  • DOI: https://doi.org/10.1016/s0969-2126(00)00159-3
  • Primary Citation of Related Structures:  
    1ET4

  • PubMed Abstract: 

    The 3.0 A crystal structure of the vitamin B(12) RNA aptamer revealed an unusual tertiary structure that is rich in novel RNA structural motifs. Important details of the interactions that stabilize noncanonical base pairing and the role of solvent in the structure were not apparent owing to the limited resolution.

    • Organizational Affiliation: 

    Department of Biology, Center for the Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA APTAMER, 35-MER
A, B, C, D, E
35N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.27α = 90
b = 98.08β = 90
c = 217.97γ = 90
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-12-28
    Changes: Advisory
  • Version 2.0: 2021-08-18
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-07
    Changes: Data collection