5ONG Dna Binding Protein date Aug 03, 2017
title X-Ray Crystal Structure Of A Nucleosome Core Particle With I Site-Specifically Crosslinked To The Histone Octamer
authors T.D.Frouws, P.D.Barth, T.J.Richmond
compound source
Molecule: Dna (147-Mer)
Chain: I
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Dh10b
Expression_system_vector_type: Plasmid
Expression_system_vector: Puc57

Molecule: Dna (147-Mer)
Chain: J
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_variant: Dh10b
Expression_system_vector_type: Plasmid
Expression_system_vector: Puc57

Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a

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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a

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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Plyss
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet3a
symmetry Space Group: P 21 21 21
R_factor 0.206 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.240 183.130 109.490 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CL, G47, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceSite-Specific Disulfide Crosslinked Nucleosomes with Enhanced Stability., Frouws TD, Barth PD, Richmond TJ, J Mol Biol. 2017 Nov 4. pii: S0022-2836(17)30522-3. doi:, 10.1016/j.jmb.2017.10.029. PMID:29113904
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (535 Kb) [Save to disk]
  • Biological Unit Coordinates (5ong.pdb1.gz) 517 Kb
  • LPC: Ligand-Protein Contacts for 5ONG
  • CSU: Contacts of Structural Units for 5ONG
  • Structure Factors (386 Kb)
  • Retrieve 5ONG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ONG from S2C, [Save to disk]
  • View 5ONG 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 5ONG
  • 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 5ong from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ong_G] [5ong_E] [5ong_D] [5ong_C] [5ong_I] [5ong_H] [5ong_F] [5ong_B] [5ong_J] [5ong_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ONG
  • Community annotation for 5ONG at PDBWiki (http://pdbwiki.org)

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