5XF6 Structural Protein Dna date Apr 07, 2017
title Nucleosome Core Particle With An Adduct Of A Binuclear Rapta Arene-Phosphaadamantane) Compound Having An Ethylenediamine
authors Z.Ma, Z.Adhireksan, B.S.Murray, P.J.Dyson, C.A.Davey
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Hist1h2aj, Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Dna (145-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 21 21 21
R_factor 0.208 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.840 109.729 182.527 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.63 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceNucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation., Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA, Nat Commun. 2017 Nov 17;8(1):1575. doi: 10.1038/s41467-017-01680-4. PMID:29146919
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (252 Kb) [Save to disk]
  • Biological Unit Coordinates (5xf6.pdb1.gz) 245 Kb
  • CSU: Contacts of Structural Units for 5XF6
  • Structure Factors (1138 Kb)
  • Retrieve 5XF6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5XF6 from S2C, [Save to disk]
  • View 5XF6 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5XF6
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5xf6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5xf6_J] [5xf6_G] [5xf6_F] [5xf6_I] [5xf6_A] [5xf6_E] [5xf6_B] [5xf6_C] [5xf6_H] [5xf6_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5XF6
  • Community annotation for 5XF6 at PDBWiki (http://pdbwiki.org)

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