3LJA Structural Protein Dna date Jan 26, 2010
title Using Soft X-Rays For A Detailed Picture Of Divalent Metal B The Nucleosome
authors B.Wu, C.A.Davey
compound source
Molecule: Histone H3.2
Chain: A, E
Engineered: Yes
 Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H4
Chain: B, F
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: C, G
Engineered: Yes
Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562

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
Expression_system_taxid: 562

Molecule: 147mer Dna
Chain: I
Engineered: Yes
Synthetic: Yes
Other_details: Sequence Based On Human Alpha-Satellite Dna

Molecule: 147mer Dna
Chain: J
Engineered: Yes
Synthetic: Yes
Other_details: Sequence Based On Human Alpha-Satellite Dna
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.259
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.348 109.785 182.424 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.75 Å
ligand MN, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceUsing Soft X-Rays for a Detailed Picture of Divalent Metal Binding in the Nucleosome., Wu B, Davey CA, J Mol Biol. 2010 Mar 27. PMID:20350553
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (3lja.pdb1.gz) 240 Kb
  • LPC: Ligand-Protein Contacts for 3LJA
  • CSU: Contacts of Structural Units for 3LJA
  • Structure Factors (841 Kb)
  • Retrieve 3LJA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LJA from S2C, [Save to disk]
  • Re-refined 3lja structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3LJA 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 3LJA
  • 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
  • 3D motif for 3LJA, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lja_I] [3lja_B] [3lja_A] [3lja_J] [3lja_D] [3lja_C] [3lja_E] [3lja] [3lja_G] [3lja_F] [3lja_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3LJA: [H2A] [H2B] [H3] [H4 ] by SMART
    • Other resources with information on 3LJA
  • Community annotation for 3LJA 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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