3X1S Structural Protein Dna date Nov 27, 2014
title Crystal Structure Of The Nucleosome Core Particle
authors P.Sivaraman, T.S.Kumarevel
compound source
Molecule: Histone H3.1
Chain: A, E
Synonym: Histone H3a, Histone H3b, Histone H3c, Histone Histone H3f, Histone H3h, Histone H3i, Histone H3j, His Histone H3l;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2a, H3fa, H3fb, H3fc, H3fd, H3ff, H3fh, H3fi, H3fj, H3fl, Hist1h3a, Hist1h3b, Hist1h3c, Hist1h3d, Hist1h3e, His Hist1h3g, Hist1h3h, Hist1h3i, Hist1h3j;
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Pgem

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

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2b, H4a, H4b, H4c, H4d, H4e, H4g, H4h, H4i, H4k, H4m, H4n, H4o, H4f2, H4fa, H4fb, H4fc, H4fd, H4fe, H4fh, H4fi, H4fj, H4fk, H4fm, H4fn, H4fo, Hist1h4a, Hist1h4 Hist1h4c, Hist1h4d, Hist1h4e, Hist1h4f, Hist1h4h, Hist1h4i, Hist1h4j, Hist1h4k, Hist1h4l, Hist2h4, Hist2h4a, Hist2h4b,
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2a Type 1-Be
Chain: C, G
Synonym: Histone H2a.2, Histone H2aa, Histone H2am
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2afa, H2afm, H3.1, Hist1h2ab, Hist1h2ae
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Histone H2b Type 1-B
Chain: D, H
Synonym: Histone H2b.1, Histone H2b.F, H2bf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: H2bff, H2bfq, H4, Hist1h2bb, Hist2h2be
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (146-Mer)
Chain: I, J
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic
Organism_taxid: 32630
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.381 109.363 175.572 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.81 Å
ligand CL, MN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (3x1s.pdb1.gz) 240 Kb
  • LPC: Ligand-Protein Contacts for 3X1S
  • CSU: Contacts of Structural Units for 3X1S
  • Structure Factors (1060 Kb)
  • Retrieve 3X1S in mmCIF format [Save to disk]
  • Re-refined 3x1s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X1S 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 3X1S
  • 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
  • Fold representative 3x1s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x1s_B] [3x1s_F] [3x1s] [3x1s_C] [3x1s_J] [3x1s_E] [3x1s_A] [3x1s_I] [3x1s_G] [3x1s_D] [3x1s_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3X1S: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 3X1S
  • Community annotation for 3X1S at PDBWiki (http://pdbwiki.org)

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