1S32 Structural Protein Dna date Jan 12, 2004
title Molecular Recognition Of The Nucleosomal 'Supergroove'
authors R.S.Edayathumangalam, P.Weyermann, J.M.Gottesfeld, P.B.Dervan, K
compound source
Molecule: Palindromic Alpha-Satellite 146 Bp Dna Fragment
Chain: I, 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
Gene: Histone H3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Based

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

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Histone H4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Based

Molecule: Histone H2a
Chain: C, G
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Histone H2a
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Based

Molecule: Histone H2b
Chain: D, H
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Gene: Histone H2b.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 De3 Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Based
symmetry Space Group: P 21 21 21
R_factor 0.219 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.352 109.717 181.827 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand ABU, BAL, CL, DIB, IMT, MN, OGG, PYB enzyme
related structures by homologous chain: 1HQ3, 1KX3
Gene
Ontology
ChainFunctionProcessComponent
A, E


C, G


F, B


H, D


Primary referenceMolecular recognition of the nucleosomal "supergroove"., Edayathumangalam RS, Weyermann P, Gottesfeld JM, Dervan PB, Luger K, Proc Natl Acad Sci U S A 2004 May 4;101(18):6864-9. Epub 2004 Apr 20. PMID:15100411
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (281 Kb) [Save to disk]
  • Biological Unit Coordinates (1s32.pdb1.gz) 272 Kb
  • LPC: Ligand-Protein Contacts for 1S32
  • CSU: Contacts of Structural Units for 1S32
  • Likely Quarternary Molecular Structure file(s) for 1S32
  • Structure Factors (1903 Kb)
  • Retrieve 1S32 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1S32 from S2C, [Save to disk]
  • Re-refined 1s32 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1S32 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 1S32
  • 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 1S32, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1s32a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1s32b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1s32c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1s32d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1s32e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1s32f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1s32g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1s32h_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1s32 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1s32_J] [1s32_B] [1s32_G] [1s32_H] [1s32_D] [1s32_I] [1s32_E] [1s32_C] [1s32] [1s32_A] [1s32_F]
  • SWISS-PROT database: [P06897] [P02281] [P84233] [P62799]
  • Domain organization of [H2A1_XENLA] [H2B11_XENLA] [H32_XENLA] [H4_XENLA] by SWISSPFAM
  • Domains found in 1S32: [H2A] [H2B] [H3] [H4 ] by SMART
  • Other resources with information on 1S32
  • Community annotation for 1S32 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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