5C8E Transcription Regulator Dna date Jun 25, 2015
title Crystal Structure Of Thermus Thermophilus Carh Bound To Adenosylcobalamin And A 26-Bp Dna Segment
authors M.Jost, C.L.Drennan
compound source
Molecule: Light-Dependent Transcriptional Regulator Carh
Chain: A, B, C, D, E, F, G, H
Engineered: Yes
Organism_scientific: Thermus Thermophilus (Strain Hb27 At 163 Dsm 7039);
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

Molecule: 26-Mer Dna Segment Containing The Carh Operator S (Antisense Strand);
Chain: I, K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus Hb27
Organism_taxid: 262724

Molecule: 26-Mer Dna Segment Containing The Carh Operator S (Sense Strand);
Chain: J, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus Hb27
Organism_taxid: 262724
symmetry Space Group: P 21 21 2
R_factor 0.250 R_Free 0.257
crystal
cell
length a length b length c angle alpha angle beta angle gamma
177.940 141.820 162.690 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.89 Å
ligand 5AD, B12 enzyme
Gene TT
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, H, C, D, G


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] (772 Kb) [Save to disk]
  • Biological Unit Coordinates (5c8e.pdb1.gz) 381 Kb
  • Biological Unit Coordinates (5c8e.pdb2.gz) 377 Kb
  • LPC: Ligand-Protein Contacts for 5C8E
  • CSU: Contacts of Structural Units for 5C8E
  • Structure Factors (327 Kb)
  • Retrieve 5C8E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5C8E from S2C, [Save to disk]
  • Re-refined 5c8e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5C8E 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 5C8E
  • 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 5c8e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5c8e_A] [5c8e_C] [5c8e_F] [5c8e_K] [5c8e] [5c8e_D] [5c8e_B] [5c8e_L] [5c8e_E] [5c8e_I] [5c8e_H] [5c8e_J] [5c8e_G]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5C8E: [HTH_MERR ] by SMART
  • Other resources with information on 5C8E
  • Community annotation for 5C8E at PDBWiki (http://pdbwiki.org)

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