RCSB PDB

218,500 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

1D65

MOLECULAR STRUCTURE OF THE B-DNA DODECAMER D(CGCAAATTTGCG)2; AN EXAMINATION OF PROPELLER TWIST AND MINOR-GROOVE WATER STRUCTURE AT 2.2 ANGSTROMS RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb1D65/pdb
NAKB: 1D65

Classification: DNA
Mutation(s): No

Deposited: 1992-03-02 Released: 1993-01-15
Deposition Author(s): Edwards, K.J., Brown, D.G., Spink, N., Neidle, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.

Edwards, K.J., Brown, D.G., Spink, N., Skelly, J.V., Neidle, S.

(1992) J Mol Biol 226: 1161-1173

PubMed: 1518049 Search on PubMed
DOI: https://doi.org/10.1016/0022-2836(92)91059-x
Primary Citation of Related Structures:
1D65

PubMed Abstract:

The crystal structure of the dodecanucleotide duplex d(CGCAAATTTGCG)2 has been solved to 2.2 A resolution and refined to an R-factor of 18.1% with the inclusion of 71 water molecules. The structure shows propeller twists of up to -20 degrees for the A.T base-pairs, although there is probably only one (weak) three-centre hydrogen bond in the six base-pair AT narrow minor-groove region. An extensive ribbon of hydration has been located in this groove that has features distinctive from the classic "spine of hydration". Solvation around phosphate groups is described, with several instances of water molecules bridging between phosphates.

Organizational Affiliation

Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.

Macromolecule Content

Total Structure Weight: 7.32 kDa
Atom Count: 557
Modelled Residue Count: 24
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPGPCPAPAPAPTPTPTPGPCPG)-3')	A, B	12	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Observed: 0.181
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.87	α = 90
b = 40.9	β = 90
c = 65.64	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1993-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1993-01-15
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references

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