5C8A Transcriptional Regulator date Jun 25, 2015
title Crystal Structure Of A Truncated Form Of Thermus Thermophilu Bound To Adenosylcobalamin (Dark State)
authors M.Jost, C.L.Drennan
compound source
Molecule: Light-Dependent Transcriptional Regulator Carh
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Thermus Thermophilus
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039
Gene: Tt_p0056
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Star Plyss
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: P 21 21 21
R_factor 0.183 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.430 99.680 143.990 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.15 Å
ligand 5AD, B12, GOL enzyme
Gene TT
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural basis for gene regulation by a B-dependent photoreceptor., Jost M, Fernandez-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PY, Kang G, Padmanabhan S, Elias-Arnanz M, Drennan CL, Nature. 2015 Sep 28. doi: 10.1038/nature14950. PMID:26416754
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (265 Kb) [Save to disk]
  • Biological Unit Coordinates (5c8a.pdb1.gz) 256 Kb
  • LPC: Ligand-Protein Contacts for 5C8A
  • CSU: Contacts of Structural Units for 5C8A
  • Structure Factors (349 Kb)
  • Retrieve 5C8A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C8A from S2C, [Save to disk]
  • Re-refined 5c8a structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5C8A 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 5C8A
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c8a_B] [5c8a] [5c8a_D] [5c8a_C] [5c8a_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5C8A
  • Community annotation for 5C8A at PDBWiki (http://pdbwiki.org)

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