8PIP | pdb_00008pip

DNA triplex structure with Polypyridyl Ruthenium Complexes

PDB DOI: https://doi.org/10.2210/pdb8PIP/pdb
NAKB: 8PIP

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

Deposited: 2023-06-22 Released: 2024-07-10
Deposition Author(s): Abdullrahman, A., Cardin, C.J., Hall, J.P.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.259 (Depositor), 0.257 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8PIP

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

Literature

DNA triplex structure with bound ruthenium polypyridyl complexes

Abdullrahman, A., McQuaid, K., Cardin, C.J., Hall, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 11.69 kDa
Atom Count: 896
Modeled Residue Count: 31
Deposited Residue Count: 31
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (31-MER)	A	31	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RKP Query on RKP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	Lambda-Ru(phen)2(dppz) complex C₄₂ H₂₆ N₈ Ru OYSRBLHMGIHFCB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
0TN Query on 0TN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	Delta-Ru(phen)2(dppz) complex C₄₂ H₂₆ N₈ Ru OYSRBLHMGIHFCB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL (Subject of Investigation/LOI) Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.259 (Depositor), 0.257 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.464	α = 90
b = 86.151	β = 90
c = 87.852	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
SHELXDE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-10

Deposition Author(s):

Abdullrahman, A.

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	H2020-MSCA-ITN-2019-861381

Revision History (Full details and data files)

Version 1.0: 2024-07-10
Type: Initial release
Version 1.1: 2024-07-24
Changes: Derived calculations

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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.