8ASK | pdb_00008ask

Crystal structure of d(GCCCACCACGGC)

• PDB DOI: https://doi.org/10.2210/pdb8ASK/pdb
• NAKB: 8ASK

• Classification: DNA
• Organism(s): DNA molecule
• Expression System: Synthesium
• Mutation(s): No 


• Deposited: 2022-08-19 Released: 2023-01-18 
• Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L., Rusev, R., Heroux, A., Doukov, T., Kuvandjiev, N.
• Funding Organization(s): The Bulgarian National Science Fund (BNSF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.125 (Depositor), 0.129 (DCC) 

Starting Model: other

Literature

Structural Characterization of Alzheimer DNA Promoter Sequences from the Amyloid Precursor Gene in the Presence of Thioflavin T and Analogs

Sbirkova-Dimitrova, H., Rusew, R., Kuvandjiev, N., Heroux, A., Doukov, T., Shivachev, B.L.

(2022) Crystals (Basel) 12

• DOI: https://doi.org/10.3390/cryst12121717

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.33 kDa 
• Atom Count: 492 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*CP*CP*AP*CP*CP*AP*CP*GP*GP*C)-3')	A [auth AAA]	12	DNA molecule

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*CP*CP*GP*TP*GP*GP*TP*GP*GP*GP*C)-3')	B [auth BBB]	12	DNA molecule

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.230 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.125 (Depositor), 0.129 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.49	α = 90
b = 64.49	β = 90
c = 46.19	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-01-18 
Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L., Rusev, R., Heroux, A., Doukov, T., Kuvandjiev, N.

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Funding Organization	Location	Grant Number
The Bulgarian National Science Fund (BNSF)	Bulgaria	KP-06-M31/1

Revision History  

• Version 1.0: 2023-01-18
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Refinement description