5F99 Dna Binding Protein date Dec 09, 2015
title X-Ray Structure Of The Mmtv-A Nucleosome Core Particle
authors T.D.Frouws, T.J.Richmond
compound source
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_plasmid: Pet3a

Molecule: Histone H4
Chain: B, F
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_plasmid: Pet3a

Molecule: Histone H2a Type 1
Chain: C, G
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_plasmid: 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_plasmid: Pet3a

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

Organism_scientific: Mouse Mammary Tumor Virus
Organism_taxid: 11757
Expression_system: Escherichia Coli
Expression_system_taxid: 316385
Expression_system_strain: Dh10b
Expression_system_plasmid: Puc57

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

Organism_scientific: Mouse Mammary Tumor Virus
Organism_taxid: 11757
Expression_system: Escherichia Coli
Expression_system_taxid: 316385
Expression_system_strain: Dh10b
Expression_system_plasmid: Puc57
symmetry Space Group: P 21 21 21
R_factor 0.175 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.873 178.915 109.061 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.63 Å
ligand CL, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceX-ray structure of the MMTV-A nucleosome core., Frouws TD, Duda SC, Richmond TJ, Proc Natl Acad Sci U S A. 2016 Jan 19. pii: 201524607. PMID:26787910
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (278 Kb) [Save to disk]
  • Biological Unit Coordinates (5f99.pdb1.gz) 271 Kb
  • LPC: Ligand-Protein Contacts for 5F99
  • CSU: Contacts of Structural Units for 5F99
  • Structure Factors (507 Kb)
  • Retrieve 5F99 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F99 from S2C, [Save to disk]
  • Re-refined 5f99 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5F99 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 5F99
  • 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 5f99 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f99_F] [5f99_J] [5f99_C] [5f99_D] [5f99_I] [5f99] [5f99_A] [5f99_E] [5f99_B] [5f99_G] [5f99_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5F99: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 5F99
  • Community annotation for 5F99 at PDBWiki (http://pdbwiki.org)

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