1D93

STRUCTURAL VARIATION IN D(CTCTAGAG). IMPLICATIONS FOR PROTEIN-DNA INTERACTIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions.

Hunter, W.N.D'Estaintot, B.L.Kennard, O.

(1989) Biochemistry 28: 2444-2451


  • PubMed Abstract: 
  • Single-crystal X-ray diffraction techniques have been used to characterize the structure of the self-complementary DNA oligomer d(CTCTAGAG). The structure was refined to an R factor of 14.7% using data to 2.15-A resolution. The tetragonal unit cell, ...

    Single-crystal X-ray diffraction techniques have been used to characterize the structure of the self-complementary DNA oligomer d(CTCTAGAG). The structure was refined to an R factor of 14.7% using data to 2.15-A resolution. The tetragonal unit cell, space group P4(3)2(1)2, has dimensions a = 42.53 and c = 24.33 A. The asymmetric unit consists of a single strand or four base pairs. Two strands, related by a crystallographic dyad axis, coil about each other to form a right-handed duplex. This octamer duplex has a mean helix rotation of 32 degrees, 11.3 base pairs per turn, an average rise of 3.1 A, C3'-endo furanose conformations, a shallow minor groove, and a deep major groove. Such averaged parameters suggest classification of the octamer as a member of the A-DNA family. However, the global parameters tend to mask variations in conformational parameters observed at the level of the base pairs. In particular, the central TpA (= TpA) step displays extensive interstrand purine-purine overlap and an unusual sugar-phosphate backbone conformation. These structural features may be directly related to certain sequence-specific protein-DNA interactions involving nucleases and repressors.


    Organizational Affiliation

    University Chemical Laboratory, Cambridge, U.K.




Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3')A8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 42.520α = 90.00
b = 42.520β = 90.00
c = 24.330γ = 90.00
Software Package:
Software NamePurpose
NUCLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance