3LZ0 Structural Protein Dna date Mar 01, 2010
title Crystal Structure Of Nucleosome Core Particle Composed Of Th 601 Dna Sequence (Orientation 1)
authors D.Vasudevan, E.Y.D.Chua, 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
Expression_system_strain: Bl21(Plyss)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3d

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
Expression_system_strain: Bl21(Plyss)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2a
Chain: C, G
Fragment: Residues 2-120
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(Plyss)
Expression_system_vector_type: Plasmid
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
Expression_system_taxid: 562
Expression_system_strain: Bl21(Plyss)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

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

Synthetic: Yes
Other_details: Synthetic Construct

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

Synthetic: Yes
Other_details: Synthetic Construct
symmetry Space Group: P 21 21 21
R_factor 0.268 R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
107.370 109.660 175.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceCrystal Structures of Nucleosome Core Particles Containing the '601' Strong Positioning Sequence., Vasudevan D, Chua EY, Davey CA, J Mol Biol. 2010 Aug 26. PMID:20800598
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (243 Kb) [Save to disk]
  • Biological Unit Coordinates (3lz0.pdb1.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 3LZ0
  • CSU: Contacts of Structural Units for 3LZ0
  • Structure Factors (3355 Kb)
  • Retrieve 3LZ0 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3LZ0 from S2C, [Save to disk]
  • Re-refined 3lz0 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3LZ0 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 3LZ0
  • 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 3LZ0, from MSDmotif at EBI
  • Fold representative 3lz0 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3lz0_F] [3lz0_A] [3lz0_C] [3lz0_B] [3lz0_D] [3lz0] [3lz0_E] [3lz0_G] [3lz0_I] [3lz0_J] [3lz0_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3LZ0: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3LZ0
  • Community annotation for 3LZ0 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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