3UYB | pdb_00003uyb

X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGTACCGA)

PDB DOI: https://doi.org/10.2210/pdb3UYB/pdb
Entry: 3UYB supersedes: 3UYA
NAKB: 3UYB

Classification: DNA
Mutation(s): No

Deposited: 2011-12-06 Released: 2013-01-16
Deposition Author(s): Niyazi, H.N., Texeira, S.C.M., Mitchell, E.P., Cardin, J.C., Forsyth, V.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.167 (Depositor), 0.162 (DCC)
R-Value Work:
0.127 (Depositor)
R-Value Observed:
0.129 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3UYB

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of lambda-[Ru(TAP)2(dppz)]2+ with d(TCGGTACCGA)2 displaying kinking of DNA via semiintercalation.

Niyazi, H.N., O'Sullivan, K., Texeira, S.C.M., Mitchell, E.P., Kelly, J.M., Cardin, J.C., Forsyth, V.T.

To be published.

Macromolecule Content

Total Structure Weight: 4.68 kDa
Atom Count: 376
Modeled Residue Count: 10
Deposited Residue Count: 10
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
5'-D(TPCPGPGPTPAPCPCPGPA)-3'	A	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RKL Query on RKL 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]	Ru(tap)2(dppz) complex C₃₈ H₂₂ N₁₂ Ru PIKVAZQLFXBUSD-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]
BA Query on BA 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]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.167 (Depositor), 0.162 (DCC)
R-Value Work: 0.127 (Depositor)
R-Value Observed: 0.129 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.376	α = 90
b = 54.376	β = 90
c = 28.995	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-01-16

Deposition Author(s):

Texeira, S.C.M.

This entry supersedes: 3UYA

Revision History (Full details and data files)

Version 1.0: 2013-01-16
Type: Initial release
Version 1.1: 2015-04-29
Changes: Other
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-03-20
Changes: Data collection, Database references, 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.