3B6F Structural Protein Dna date Oct 29, 2007
title Nucleosome Core Particle Treated With Cisplatin
authors B.Wu, C.A.Davey
compound source
Molecule: Histone H3.2
Chain: A, E
Synonym: Histone H3
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(De3)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(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2a
Chain: C, G
Synonym: Histone H2a.1
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Loc494591
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Histone H2b 1.1
Chain: D, H
Synonym: H2b1.1, Histone H2b.2
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(De3)Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: 147-Mer Dna
Chain: I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19

Molecule: 147-Mer Dna
Chain: J
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb101
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19
symmetry Space Group: P 21 21 21
R_factor 0.330 R_Free 0.402
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.327 109.380 180.585 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.45 Å
ligand MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceSite selectivity of platinum anticancer therapeutics., Wu B, Droge P, Davey CA, Nat Chem Biol. 2008 Feb;4(2):110-2. Epub 2007 Dec 23. PMID:18157123
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (3b6f.pdb1.gz) 242 Kb
  • LPC: Ligand-Protein Contacts for 3B6F
  • CSU: Contacts of Structural Units for 3B6F
  • Likely Quarternary Molecular Structure file(s) for 3B6F
  • Structure Factors (222 Kb)
  • Retrieve 3B6F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B6F from S2C, [Save to disk]
  • Re-refined 3b6f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3B6F 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 3B6F
  • 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 3B6F, from MSDmotif at EBI
  • Fold representative 3b6f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b6f_G] [3b6f_A] [3b6f] [3b6f_E] [3b6f_J] [3b6f_H] [3b6f_B] [3b6f_I] [3b6f_F] [3b6f_D] [3b6f_C]
  • SWISS-PROT database: [P06897] [P02281] [P84233] [P62799]
  • Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H32_XENLA] [H4_XENLA] by SWISSPFAM
  • Domains found in 3B6F: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3B6F
  • Community annotation for 3B6F 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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