7EAQ | pdb_00007eaq

DNA quadruplex composed of i-motif and Z-DNA

• PDB DOI: https://doi.org/10.2210/pdb7EAQ/pdb
• NAKB: 7EAQ

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2021-03-08 Released: 2022-03-09 
• Deposition Author(s): Kondo, J., Igarashi, Y.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.296 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Literature

DNA quadruplex composed of i-motif and Z-DNA

Kondo, J., Igarashi, Y.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.25 kDa 
• Atom Count: 495 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*AP*CP*CP*TP*CP*GP*CP*G)-3')	A, B	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.296 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.129	α = 90
b = 30.129	β = 90
c = 174.064	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): Kondo, J., Igarashi, Y.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	24245037

Revision History  

• Version 1.0: 2022-03-09
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection