3Q5C | pdb_00003q5c

Crystal structure of four-way junction with sticky end

• PDB DOI: https://doi.org/10.2210/pdb3Q5C/pdb
• NAKB: 3Q5C

• Classification: DNA
• Mutation(s): No 


• Deposited: 2010-12-28 Released: 2011-05-18 
• Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice

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

(2011) Biochem Biophys Res Commun 407: 548-551

• PubMed: 21419105 
• DOI: https://doi.org/10.1016/j.bbrc.2011.03.056
• Primary Citation Related Structures: 
  3Q5C


• PubMed Abstract: 
  

  We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind to each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5Å. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.

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Organizational Affiliation: 
• CAS in Crystallography and Biophysics, University of Madras, Chennai 600 025, India.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 12.19 kDa 
• Atom Count: 817 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique nucleic acid chains: 1

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.64	α = 112.77
b = 33.841	β = 90
c = 40.4	γ = 110.44

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Venkadesh, S., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description