3DZD Transcription Regulator date Jul 29, 2008
title Crystal Structure Of Sigma54 Activator Ntrc4 In The Inactive
authors J.D.Batchelor, M.Doucleff, C.J.Lee, K.Matsubara, S.De Carlo, J.H M.M.Lamers, J.G.Pelton, D.E.Wemmer
compound source
Molecule: Transcriptional Regulator (Ntrc Family)
Chain: A, B
Fragment: Unp Residues 2 To 369
Engineered: Yes
 Organism_scientific: Aquifex Aeolicus
Organism_taxid: 63363
Gene: Aq_164, Ntrc4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pskb3
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.897 93.105 114.163 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand ADP, MSE, NA enzyme
Gene AQ
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure and Regulatory Mechanism of Aquifex aeolicus NtrC4: Variability and Evolution in Bacterial Transcriptional Regulation., Batchelor JD, Doucleff M, Lee CJ, Matsubara K, De Carlo S, Heideker J, Lamers MH, Pelton JG, Wemmer DE, J Mol Biol. 2008 Oct 17. PMID:18955063
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (256 Kb) [Save to disk]
  • Biological Unit Coordinates (3dzd.pdb1.gz) 251 Kb
  • LPC: Ligand-Protein Contacts for 3DZD
  • CSU: Contacts of Structural Units for 3DZD
  • Likely Quarternary Molecular Structure file(s) for 3DZD
  • Structure Factors (342 Kb)
  • Retrieve 3DZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DZD from S2C, [Save to disk]
  • Re-refined 3dzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3DZD 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 3DZD
  • 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
  • 3D motif for 3DZD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dzd_A] [3dzd] [3dzd_B]
  • SWISS-PROT database: [O66551]
  • Domain organization of [O66551_AQUAE] by SWISSPFAM
  • Domains found in 3DZD: [AAA] [REC ] by SMART
    • Other resources with information on 3DZD
  • Community annotation for 3DZD 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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