4XUJ

Nucleosome core particle containing adducts from treatment with a thiomorpholine-substituted [(eta-6-p-cymene)Ru(3-hydroxy-2-pyridone)Cl] compound

PDB DOI: https://doi.org/10.2210/pdb4XUJ/pdb
NAKB: 4XUJ

Classification: DNA-BINDING PROTEIN/DNA
Organism(s): Xenopus laevis, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-01-26 Released: 2016-01-27
Deposition Author(s): Adhireksan, Z., Davey, C.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.299
R-Value Work: 0.263
R-Value Observed: 0.265

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Contrasting Cytotoxicity and Reactivity of RuII-Arene Complexes of Morpholine vs Thiomorpholine Substituted 3-Hydroxy-2-pyridone Ligands

Hanif, M., Meier, S.M., Adhireksan, Z., Henke, H., Martic, S., Labib, M., Kandioller, W., Jakupec, M.A., Kraatz, H.B., Davey, C.A., Keppler, B.K., Hartinger, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 199.15 kDa
Atom Count: 12,075
Modelled Residue Count: 1,055
Deposited Residue Count: 1,270
Unique protein chains: 4
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84233
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	128	Xenopus laevis	Mutation(s): 0 Gene Names: hist1h2aj, LOC494591
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	125	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	I	145	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (145-MER)	J	145	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4A6 Query on 4A6 Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain P [auth H] SDF format, chain Q [auth H] MOL2 format, chain L [auth D] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H]	L [auth D], P [auth H], Q [auth H]	[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)benzene]ruthenium C₁₀ H₁₄ Ru UGCPEEMQJJGXOS-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain P [auth H] Focus chain Q [auth H] Interactions & Density Focus chain L [auth D] Focus chain P [auth H] Focus chain Q [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth G] SDF format, chain O [auth H] MOL2 format, chain K [auth C] MOL2 format, chain N [auth G] MOL2 format, chain O [auth H]	K [auth C], N [auth G], O [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth C] Focus chain N [auth G] Focus chain O [auth H] Interactions & Density Focus chain K [auth C] Focus chain N [auth G] Focus chain O [auth H]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth E] MOL2 format, chain M [auth E]	M [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Interactions & Density Focus chain M [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.299
R-Value Work: 0.263
R-Value Observed: 0.265
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.426	α = 90
b = 109.754	β = 90
c = 181.277	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Adhireksan, Z.

Davey, C.A.

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2016-03-02
Changes: Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description