2X6V Transcription Dna date Feb 22, 2010
title Crystal Structure Of Human Tbx5 In The Dna-Bound And Dna- Free Form
authors D.Ptchelkine, C.U.Stirnimann, C.Grimm, C.W.Mueller
compound source
Molecule: T-Box Transcription Factor Tbx5
Chain: A, B
Fragment: T-Box Domain, Residues 51-251
Synonym: T-Box Protein 5, Human Tbx5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_plasmid: Pprox Htb

Molecule: 5'-D(Tpcptpcpapcpapcpcptptp)-3'
Chain: C

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpapapgpgptpgptpgpapgp)-3'
Chain: D

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 61 2 2
R_factor 0.1973 R_Free 0.2252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
118.240 118.240 243.000 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand MG, PE4 enzyme
note 2X6V is a representative structure
Primary referenceStructural basis of TBX5-DNA recognition: the T-box domain in its DNA-bound and -unbound form., Stirnimann CU, Ptchelkine D, Grimm C, Muller CW, J Mol Biol. 2010 Jul 2;400(1):71-81. Epub 2010 May 5. PMID:20450920
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (83 Kb) [Save to disk]
  • Biological Unit Coordinates (2x6v.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 2X6V
  • CSU: Contacts of Structural Units for 2X6V
  • Structure Factors (394 Kb)
  • Retrieve 2X6V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X6V from S2C, [Save to disk]
  • Re-refined 2x6v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X6V 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 2X6V
  • 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 2X6V, from MSDmotif at EBI
  • Fold representative 2x6v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x6v_A] [2x6v_B] [2x6v_C] [2x6v] [2x6v_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2X6V: [TBOX ] by SMART
  • Other resources with information on 2X6V
  • Community annotation for 2X6V 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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