1O55

MOLECULAR STRUCTURE OF TWO CRYSTAL FORMS OF CYCLIC TRIADENYLIC ACID AT 1 ANGSTROM RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular structure of two crystal forms of cyclic triadenylic acid at 1A resolution.

Gao, Y.G.Robinson, H.Guan, Y.Liaw, Y.C.van Boom, J.H.van der Marel, G.A.Wang, A.H.

(1998) J.Biomol.Struct.Dyn. 16: 69-76

  • DOI: 10.1080/07391102.1998.10508228
  • Primary Citation of Related Structures:  1O56, 416D, 415D

  • PubMed Abstract: 
  • The three dimensional structures of cyclic deoxytriadenylic acid, c-d(ApApAp), from two different trigonal crystal forms (space groups P3 and R32) have been determined by x-ray diffraction analysis at 1A resolution. Both structures were solved by dir ...

    The three dimensional structures of cyclic deoxytriadenylic acid, c-d(ApApAp), from two different trigonal crystal forms (space groups P3 and R32) have been determined by x-ray diffraction analysis at 1A resolution. Both structures were solved by direct methods and refined by anisotropic least squares refinement to R-factors of 0.109 and 0.137 for the P3 and R32 forms, respectively. In both crystal forms, each of the two independent c-d(ApApAp) molecules sits on the crystallographic 3-fold axis. All four independent c-d(ApApAp) molecules have similar backbone conformations. The deoxyriboses are in the S-type pucker with pseudorotation angles ranging from 156.7 degrees to 168.6 degrees and the bases have anti glycosyl torsion angles (chi falling in two ranges, one at -104.3 degrees and the other ranging from -141.0 degrees to -143.8 degrees). In the R32 form, a hexahydrated cobalt(II) ion is found to coordinate through bridging water molecules to N1, N3, and N7 atoms of three adjacent adenines and oxygen atoms of phosphates. Comparison with other structures of cyclic oligonucleotides indicates that the sugar adopts N-type pucker in cyclic dinucleotides and S-type pucker in cyclic trinucleotides, regardless whether the sugar is a ribose or a deoxyribose.


    Organizational Affiliation

    Department of Cell & Structural Biology, University of Illinois at Urbana-Champaign, Urbana 61801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-CD(*AP*AP*AP)-3')A,B3N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 22.637α = 90.00
b = 22.637β = 90.00
c = 44.581γ = 120.00
Software Package:
Software NamePurpose
bioteXdata collection
SHELXL-97refinement
bioteXdata reduction
SHELXSphasing
bioteXdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description