5OXV Gene Regulation date Sep 07, 2017
title Structure Of The 4_601_157 Tetranucleosome (C2 Form)
authors B.Ekundayo, T.Schalch
compound source
Molecule: Dna Strand 1 (601-Based Sequence Model)
Chain: J
Engineered: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b 1.1
Chain: R, N, H, D
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: Histone H2a
Chain: Q, M, G, C
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 H4
Chain: P, L, F, B
Engineered: Yes

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

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

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

Molecule: Dna Strand 2 (601-Based Sequence Model)
Chain: I
Engineered: Yes

Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.317 R_Free 0.352
crystal
cell
length a length b length c angle alpha angle beta angle gamma
348.839 63.274 271.361 90.00 124.74 90.00
method X-Ray Diffractionresolution 6.72 Å
Gene
Ontology
ChainFunctionProcessComponent
A, O, K, E


F, P, B, L


N, H, D, R


Q, M, C, G


Primary referenceCapturing structural heterogeneity in chromatin fibers., Ekundayo B, Richmond TJ, Schalch T, J Mol Biol. 2017 Sep 9. pii: S0022-2836(17)30424-2. doi:, 10.1016/j.jmb.2017.09.002. PMID:28893533
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (475 Kb) [Save to disk]
  • Biological Unit Coordinates (5oxv.pdb1.gz) 465 Kb
  • CSU: Contacts of Structural Units for 5OXV
  • Structure Factors (157 Kb)
  • Retrieve 5OXV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OXV from S2C, [Save to disk]
  • View 5OXV 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 5OXV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5oxv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oxv_O] [5oxv_F] [5oxv_H] [5oxv_L] [5oxv_I] [5oxv_J] [5oxv_K] [5oxv_M] [5oxv_G] [5oxv_R] [5oxv_D] [5oxv_A] [5oxv_C] [5oxv_Q] [5oxv_N] [5oxv_P] [5oxv_E] [5oxv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OXV
  • Community annotation for 5OXV at PDBWiki (http://pdbwiki.org)

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