5B1L Structural Protein Dna date Dec 08, 2015
title The Mouse Nucleosome Structure Containing H3t
authors T.Urahama, S.Machida, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Tagu H.Kurumizaka
compound source
Molecule: Histone H3t
Chain: A, E
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Gm12260
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

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

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Hist1h4a, Hist1h4b, H4-53, Hist1h4c, H4-12, Hist1h4d, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4m, Hist2h4a, Hist2h4, Hist4h4;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm109(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2a Type 1
Chain: C, G
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Hist1h2ab, Hist1h2ac, Hist1h2ad, Hist1h2ae, Hist1h2ag Hist1h2ai, Hist1h2an, Hist1h2ao;
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Histone H2b Type 3-A
Chain: D, H
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Hist3h2ba
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli Dh5[Alpha]
Expression_system_taxid: 668369
Expression_system_strain: Dh5[Alpha]
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgem-T Easy
symmetry Space Group: P 21 21 21
R_factor 0.197 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
98.968 107.425 167.332 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.35 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (252 Kb) [Save to disk]
  • Biological Unit Coordinates (5b1l.pdb1.gz) 244 Kb
  • LPC: Ligand-Protein Contacts for 5B1L
  • CSU: Contacts of Structural Units for 5B1L
  • Structure Factors (1158 Kb)
  • Retrieve 5B1L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5B1L from S2C, [Save to disk]
  • Re-refined 5b1l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5B1L 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 5B1L
  • 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 5b1l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5b1l_A] [5b1l_E] [5b1l] [5b1l_I] [5b1l_H] [5b1l_B] [5b1l_J] [5b1l_F] [5b1l_G] [5b1l_C] [5b1l_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5B1L
  • Community annotation for 5B1L at PDBWiki (http://pdbwiki.org)

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