8RMH | pdb_00008rmh

Crystal structure of parallel G-quadruplex containing T-tetrads and TG-octaplet

PDB DOI: https://doi.org/10.2210/pdb8RMH/pdb
NAKB: 8RMH

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

Deposited: 2024-01-06 Released: 2025-01-15
Deposition Author(s): Abdullrahman, A., El Omari, K., Paterson, N., Orr, C., Lambert, M., Cardin, C.J., Sanchez-Weatherby, J., Hall, J.P.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.190 (Depositor), 0.185 (DCC)
R-Value Work:
0.151 (Depositor), 0.147 (DCC)
R-Value Observed:
0.154 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of parallel G-quadruplex containing T-tetrads and TG-octaplet

Abdullrahman, A., El Omari, K., Paterson, N., Orr, C., Lambert, M., Sandy, J., Mikolajek, H., Cardin, C.J., Sanchez-Weatherby, J., Hall, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 4.87 kDa
Atom Count: 366
Modeled Residue Count: 14
Deposited Residue Count: 14
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(TPGPGPTPGPGP*T)-3')	A, B	7	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.190 (Depositor), 0.185 (DCC)
R-Value Work: 0.151 (Depositor), 0.147 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.436	α = 90
b = 40.436	β = 90
c = 40.479	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
XSCALE	data scaling
ACORN	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Abdullrahman, A.

Sanchez-Weatherby, J.

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	H2020-MSCA-INT-2019-861

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

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.