4S2Q Dna Binding Protein Dna date Jan 21, 2015
title Crystal Structure Of Hmg Domain Of The Chondrogenesis Master Regulator, Sox9 In Complex With Chip-Seq Identified Dna Ele
authors S.Vivekanandan, B.Moovarkumudalvan, J.Lescar, P.R.Kolatkar
compound source
Molecule: Dna (5'- D(Papgpgpcptptptpgptptpcptpcpcptpg)-3');
Chain: A
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Transcription Factor Sox-9
Chain: D
Fragment: Unp Residues 103-178
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Sox9, Sox-9
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Petg20a
Expression_system_plasmid: Petg20a-Sox9hmg
symmetry Space Group: P 41 21 2
R_factor 0.213 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.492 99.492 45.894 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (61 Kb) [Save to disk]
  • Biological Unit Coordinates (4s2q.pdb1.gz) 57 Kb
  • CSU: Contacts of Structural Units for 4S2Q
  • Structure Factors (113 Kb)
  • Retrieve 4S2Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4S2Q from S2C, [Save to disk]
  • Re-refined 4s2q structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4S2Q 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 4S2Q
  • 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 4s2q from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4s2q_D] [4s2q] [4s2q_A] [4s2q_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4S2Q: [HMG ] by SMART
  • Other resources with information on 4S2Q
  • Community annotation for 4S2Q at PDBWiki (http://pdbwiki.org)

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