9FTA | pdb_00009fta

Crystal structure of d(GGGGTTTTGGGG) with Zn and K

• PDB DOI: https://doi.org/10.2210/pdb9FTA/pdb
• NAKB: 9FTA

• Classification: DNA
• Organism(s): DNA molecule
• Mutation(s): No 


• Deposited: 2024-06-24 Released: 2025-07-02 
• Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L.
• Funding Organization(s): Bulgarian National Science Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 
  0.426 (Depositor), 0.433 (DCC) 
• R-Value Work: 
  0.334 (Depositor), 0.338 (DCC) 

Starting Model: experimental

Literature

Crystal structure of d(GGGGTTTTGGGG) with Zn and K

Sbirkova-Dimitrova, H.I., Shivachev, B.L.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.98 kDa 
• Atom Count: 1,070 
• Modeled Residue Count: 48 
• Deposited Residue Count: 48 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	12	DNA molecule

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	K [auth AAA], M [auth BBB], N [auth BBB], T [auth DDD]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA], I [auth AAA], J [auth AAA], L [auth BBB], O [auth CCC], P [auth CCC], Q [auth CCC], R [auth CCC], S [auth CCC]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	U [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free:  0.426 (Depositor), 0.433 (DCC) 
• R-Value Work:  0.334 (Depositor), 0.338 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.457	α = 89.996
b = 47.925	β = 89.916
c = 96.076	γ = 90.059

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: 2025-07-02 
Deposition Author(s): Sbirkova-Dimitrova, H.I., Shivachev, B.L.

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Funding Organization	Location	Grant Number
Bulgarian National Science Fund	Bulgaria	KP-06-KOCT/5

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release