2NZD Structural Protein Dna date Nov 23, 2006
title Nucleosome Core Particle Containing 145 Bp Of Dna
authors M.S.Ong, T.J.Richmond, C.A.Davey
compound source
Molecule: Dna (145-Mer)
Chain: I
Engineered: Yes
Synthetic: Yes

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

Synthetic: Yes

Molecule: Histone H3
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
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b
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
symmetry Space Group: P 21 21 21
R_factor 0.233 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.617 109.856 181.217 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceDNA Stretching and Extreme Kinking in the Nucleosome Core., Ong MS, Richmond TJ, Davey CA, J Mol Biol. 2007 Mar 2;. PMID:17379244
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (249 Kb) [Save to disk]
  • Biological Unit Coordinates (2nzd.pdb1.gz) 242 Kb
  • LPC: Ligand-Protein Contacts for 2NZD
  • CSU: Contacts of Structural Units for 2NZD
  • Likely Quarternary Molecular Structure file(s) for 2NZD
  • Structure Factors (449 Kb)
  • Retrieve 2NZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NZD from S2C, [Save to disk]
  • Re-refined 2nzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NZD 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 2NZD
  • 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 2NZD, from MSDmotif at EBI
  • Fold representative 2nzd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nzd_G] [2nzd_I] [2nzd_H] [2nzd_B] [2nzd_J] [2nzd_A] [2nzd_D] [2nzd_E] [2nzd_C] [2nzd_F] [2nzd]
  • SWISS-PROT database: [P06897] [P02281] [P84233] [P62799]
  • Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H32_XENLA] [H4_XENLA] by SWISSPFAM
  • Domains found in 2NZD: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 2NZD
  • Community annotation for 2NZD 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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