3WKJ Structural Protein Dna date Oct 22, 2013
title The Nucleosome Containing Human Tsh2b
authors T.Urahama, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Kurumizaka
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a, Histone H3b, Histone H3c, Histone Histone H3f, Histone H3h, Histone H3i, Histone H3j, His Histone H3l;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H3.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H4
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-Be
Chain: C, G
Synonym: Histone H2a.2, Histone H2aa, Histone H2am
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

Molecule: Histone H2b Type 1-A
Chain: D, H
Synonym: Histone H2b, Testis, Tsh2b.1, Testis-Specific Hist
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hist1h2ba, Tsh2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phce

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

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
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 0.235 R_Free 0.291
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.037 109.926 182.961 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 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] (246 Kb) [Save to disk]
  • Biological Unit Coordinates (3wkj.pdb1.gz) 240 Kb
  • LPC: Ligand-Protein Contacts for 3WKJ
  • CSU: Contacts of Structural Units for 3WKJ
  • Structure Factors (453 Kb)
  • Retrieve 3WKJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3WKJ from S2C, [Save to disk]
  • Re-refined 3wkj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3WKJ 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 3WKJ
  • 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
  • 3D motif for 3WKJ, from MSDmotif at EBI
  • Fold representative 3wkj from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3wkj_I] [3wkj] [3wkj_A] [3wkj_B] [3wkj_E] [3wkj_G] [3wkj_F] [3wkj_J] [3wkj_D] [3wkj_H] [3wkj_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3WKJ: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3WKJ
  • Community annotation for 3WKJ at PDBWiki (http://pdbwiki.org)

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