5D8C Transcription Dna date Aug 17, 2015
title Crystal Structure Of Hinmlr, A Merr Family Regulator Lacking Sensor Domain, Bound To Promoter Dna
authors R.M.Counago, C.W.Chang, N.H.Chen, K.Y.Djoko, A.G.Mcewan, B.Kobe
compound source
Molecule: Merr Family Regulator Protein
Chain: A, B
Engineered: Yes
 Organism_scientific: Haemophilus Influenzae (Strain Atcc 51 11121 Kw20 Rd);
Organism_taxid: 71421
Strain: Atcc 51907 Dsm 11121 Kw20 Rd
Gene: Hi_0186
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21de(3)
Expression_system_plasmid: Pmcsg7

Molecule: Dna (5'- D(Cptptpapgpapgptptpcpapcptpcptpapapg)-3'
Chain: C
Engineered: Yes
Other_details: Promoter Sequence For Adhc-Estd Operon And N
Synthetic: Yes
Organism_scientific: Haemophilus Influenzae Rd Kw20
Organism_taxid: 71421

Molecule: Dna (5'- D(Cptptpapgpapgptpgpapapcptpcptpapapg)-3'
Chain: D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Haemophilus Influenzae Rd Kw20
Organism_taxid: 71421
symmetry Space Group: C 1 2 1
R_factor 0.208 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
56.030 111.820 103.170 90.00 102.10 90.00
method X-Ray Diffractionresolution 2.25 Å
Gene HI
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region., Counago RM, Chen NH, Chang CW, Djoko KY, McEwan AG, Kobe B, Nucleic Acids Res. 2016 Jun 15. pii: gkw543. PMID:27307602
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (131 Kb) [Save to disk]
  • Biological Unit Coordinates (5d8c.pdb1.gz) 120 Kb
  • CSU: Contacts of Structural Units for 5D8C
  • Structure Factors (829 Kb)
  • Retrieve 5D8C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D8C from S2C, [Save to disk]
  • Re-refined 5d8c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5D8C 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 5D8C
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d8c_D] [5d8c_A] [5d8c_B] [5d8c_C] [5d8c]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5D8C: [HTH_MERR ] by SMART
    • Other resources with information on 5D8C
  • Community annotation for 5D8C at PDBWiki (http://pdbwiki.org)

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