3T8P

Crystal structure of d(CGGGTACCCG)4 as a four-way Holliday junction

• PDB DOI: https://doi.org/10.2210/pdb3T8P/pdb
• NAKB: 3T8P

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-12-21 
• Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.278 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 

Literature

Structure of d(CGGGTACCCG)(4) as a four-way Holliday junction

Mandal, P.K., Venkadesh, S., Gautham, N.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1506-1510

• PubMed: 22139153 
• DOI: https://doi.org/10.1107/S1744309111046616
• Primary Citation of Related Structures:  
  3T8P


• PubMed Abstract: 
  

  The crystal structure of the decamer sequence d(CGGGTACCCG)(4) as a four-way Holliday junction has been determined at 2.35 Å resolution. The sequence was designed in order to understand the principles that govern the relationship between sequence and branching structure. It crystallized as a four-way junction structure with an overall geometry similar to those of previously determined Holliday junction structures.

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Organizational Affiliation: 

CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.13 kDa 
• Atom Count: 423 
• 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*GP*GP*GP*TP*AP*CP*CP*CP*G)-3')	A, B	10	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.278 
• R-Value Work: 0.235 
• R-Value Observed: 0.238 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.289	α = 90
b = 23.597	β = 111.3
c = 37.124	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Mandal, P.K., Venkadesh, S., Gautham, N.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description