3KXB Transcription Dna date Dec 02, 2009
title Structural Characterization Of H3k56q Nucleosomes And Nucleo Arrays
authors N.J.Clark, W.G.Lilyestrom
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
Mutation: Yes
Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

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

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

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

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Gene: Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1
Engineered: Yes
Mutation: Yes

Organism_scientific: Xenopus Laevis
Organism_common: Clawed Frog,Common Platanna,Platanna
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: Palindromic 146 Bp Dna Repeat 89 From Human X-Ch Alpha Satellite Dna;
Chain: I, J
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.283 R_Free 0.292
crystal
cell
length a length b length c angle alpha angle beta angle gamma
109.517 105.670 181.330 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceStructural characterization of H3K56Q nucleosomes and nucleosomal arrays., Watanabe S, Resch M, Lilyestrom W, Clark N, Hansen JC, Peterson C, Luger K, Biochim Biophys Acta. 2010 Jan 22. PMID:20100606
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (245 Kb) [Save to disk]
  • Biological Unit Coordinates (3kxb.pdb1.gz) 238 Kb
  • CSU: Contacts of Structural Units for 3KXB
  • Structure Factors (382 Kb)
  • Retrieve 3KXB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KXB from S2C, [Save to disk]
  • Re-refined 3kxb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KXB 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 3KXB
  • 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
  • 3D motif for 3KXB, from MSDmotif at EBI
  • Fold representative 3kxb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kxb_F] [3kxb_D] [3kxb_A] [3kxb_G] [3kxb] [3kxb_H] [3kxb_B] [3kxb_C] [3kxb_J] [3kxb_E] [3kxb_I]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3KXB: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3KXB
  • Community annotation for 3KXB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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