4EUW Transcription Dna date Apr 25, 2012
title Crystal Structure Of A Hmg Domain Of Transcription Factor So To Dna (Sox-9dna) From Homo Sapiens At 2.77 A Resolution
authors Joint Center For Structural Genomics (Jcsg), Partnership For Biology (Stemcell)
compound source
Molecule: Transcription Factor Sox-9
Chain: A
Fragment: Hmg Box Containing Residues 98-181
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sgt82680, Sox9
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)Phager20080807
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsf2ek6tevlic

Molecule: Dna (5'-D(Cptpcptptptpgpapgpapapg)-3'
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Sequence Matching The Sox-9 Binding Site Fro Anti-Mullerian Hormone (Amh) Promoter, Top Strand;

Molecule: Dna (5'-D(Cptptpcptpcpapapapgpapg)-3'
Chain: C
Engineered: Yes

Synthetic: Yes
Other_details: Sequence Matching The Sox-9 Binding Site Fro Anti-Mullerian Hormone (Amh) Promoter, Bottom Strand
symmetry Space Group: C 2 2 2
R_factor 0.247 R_Free 0.278
length a length b length c angle alpha angle beta angle gamma
55.772 134.654 49.987 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.77 Å
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (4euw.pdb1.gz) 46 Kb
  • CSU: Contacts of Structural Units for 4EUW
  • Structure Factors (246 Kb)
  • Retrieve 4EUW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4EUW from S2C, [Save to disk]
  • Re-refined 4euw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4EUW 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 4EUW
  • 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 4EUW, from MSDmotif at EBI
  • Fold representative 4euw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4euw_A] [4euw] [4euw_B] [4euw_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4EUW: [HMG ] by SMART
  • Other resources with information on 4EUW
  • Community annotation for 4EUW at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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