4EZ2 | pdb_00004ez2

Crystal Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4EZ2/pdb
• NAKB: 4EZ2

• Classification: DNA
• Mutation(s): No 


• Deposited: 2012-05-02 Released: 2012-10-17 
• Deposition Author(s): Chakraborty, A., Mandal, P.K., Gautham, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structure of d(CCGGGACCGG)(4) as a four-way junction at 1.6 A resolution: new insights into solvent interactions.

Chakraborty, A., Mandal, P.K., Gautham, N.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1169-1174

• PubMed: 23027741 
• DOI: https://doi.org/10.1107/S1744309112034926
• Primary Citation Related Structures: 
  4EZ2


• PubMed Abstract: 
  

  The crystal structure of the decamer sequence d(CCGGGACCGG)(4) has previously been reported at 2.16 Å resolution as a four-way junction. Here, the structure of this sequence is reported at the significantly higher resolution of 1.6 Å, which is the highest resolution reported for a four-way junction. This allowed the unambiguous identification of an extensive hydration network with distinct patterns and solvent-mediated interactions that shed new light on the role of water in the formation and stabilization of junction structures.

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

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 6.17 kDa 
• Atom Count: 503 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.01	α = 90
b = 24.35	β = 112.53
c = 38.18	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
AMoRE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-17 
Deposition Author(s): Chakraborty, A., Mandal, P.K., Gautham, N.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description