196D

CRYSTAL STRUCTURE OF C-T-C-T-C-G-A-G-A-G: IMPLICATIONS FOR THE STRUCTURE OF THE HOLLIDAY JUNCTION

• PDB DOI: https://doi.org/10.2210/pdb196D/pdb
• NAKB: 196D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1994-11-07 Released: 1995-02-27 
• Deposition Author(s): Goodsell, D.S., Grzeskowiak, K., Dickerson, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.200 

Literature

Crystal structure of C-T-C-T-C-G-A-G-A-G. Implications for the structure of the Holliday junction.

Goodsell, D.S., Grzeskowiak, K., Dickerson, R.E.

(1995) Biochemistry 34: 1022-1029

• PubMed: 7827018 
• DOI: https://doi.org/10.1021/bi00003a037
• Primary Citation of Related Structures:  
  196D


• PubMed Abstract: 
  

  The structure of the B-DNA decamer of sequence C-T-C-T-C-G-A-G-A-G shows a crossed arrangement of helices in the C2 crystal lattice. This is the fourth example of a crossed arrangement of B-DNA oligomers in a crystal, and in spite of the fact that each of these four crystallizes in a different lattice, all have nearly identical structures at the crossing contact. This ubiquitous crossing arrangement may be used to generate a structure for the Holliday junction that is fully consistent with the available physical data.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.33 kDa 
• Atom Count: 524 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*CP*TP*CP*GP*AP*GP*AP*G)-3')	A, B	10	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.23	α = 90
b = 24.32	β = 126.78
c = 40.83	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-02-27 
Deposition Author(s): Goodsell, D.S., Grzeskowiak, K., Dickerson, R.E.

Revision History  

• Version 1.0: 1995-02-27
  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, Derived calculations