190D

Crystal structure of a four-stranded intercalated DNA: d(C4)

PDB DOI: https://doi.org/10.2210/pdb190D/pdb
NAKB: 190D

Classification: DNA
Mutation(s): No

Deposited: 1994-09-02 Released: 1995-02-07
Deposition Author(s): Chen, L., Cai, L., Zhang, X., Rich, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Work: 0.218
R-Value Observed: 0.218

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a four-stranded intercalated DNA: d(C4).

Chen, L., Cai, L., Zhang, X., Rich, A.

(1994) Biochemistry 33: 13540-13546

PubMed: 7947764 Search on PubMed
DOI: https://doi.org/10.1021/bi00250a005
Primary Citation of Related Structures:
190D

PubMed Abstract:
The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

Organizational Affiliation

Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Macromolecule Content

Total Structure Weight: 8.89 kDa
Atom Count: 630
Modelled Residue Count: 32
Deposited Residue Count: 32
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(CPCPCPC)-3')	A, B, C, D, E A, B, C, D, E, F, G, H	4	N/A
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Work: 0.218
R-Value Observed: 0.218
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.3	α = 90
b = 82.3	β = 90
c = 82.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 1995-02-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1995-02-07
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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.