8ASH | pdb_00008ash

Crystal structure of d(CCGGGGTACCCCGG) with XRB

PDB DOI: https://doi.org/10.2210/pdb8ASH/pdb
NAKB: 8ASH

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., Kuvandjiev, N., Heroux, A., Doukov, T.
Funding Organization(s): Bulgarian National Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.193 (Depositor), 0.181 (DCC)
R-Value Work:
0.141 (Depositor), 0.139 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 8.88 kDa
Atom Count: 590
Modeled Residue Count: 28
Deposited Residue Count: 28
Unique nucleic acid chains: 1

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPCPGPGPGPGPTPAPCPCPCPCPGPG)-3')	A [auth AAA], B [auth BBB]	14	DNA molecule
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O89 (Subject of Investigation/LOI) Query on O89 Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] MOL2 format, chain C [auth AAA] mmCIF format, chain C [auth AAA]	C [auth AAA]	4-[(~{E})-(3,6-dimethyl-1,3-benzothiazol-2-yl)iminomethyl]-~{N},~{N}-dimethyl-aniline C₁₈ H₂₀ N₃ S YMJKNBJZXPYPNA-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Interactions & Density Focus chain C [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.193 (Depositor), 0.181 (DCC)
R-Value Work: 0.141 (Depositor), 0.139 (DCC)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.76	α = 90
b = 41.76	β = 90
c = 88.96	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Sbirkova-Dimitrova, H.I.

Shivachev, B.L.

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

Revision History (Full details and data files)

Version 1.0: 2023-01-18
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.