3ZPL

Crystal structure of Sco3205, a MarR family transcriptional regulator from Streptomyces coelicolor, in complex with DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Investigation of DNA Sequence Recognition by a Streptomycete Marr Family Transcriptional Regulator Through Surface Plasmon Resonance and X-Ray Crystallography.

Stevenson, C.E.M., Assaad, A., Chandra, G., Le, T.B.K., Greive, S.J., Bibb, M.J., Lawson, D.M.

(2013) Nucleic Acids Res. 41: 7009

  • DOI: 10.1093/nar/gkt523

  • PubMed Abstract: 

    • Consistent with their complex lifestyles and rich secondary metabolite profiles, the genomes of streptomycetes encode a plethora of transcription factors, the vast majority of which are uncharacterized. Herein, we use Surface Plasmon Resonance (SPR) ...

    Consistent with their complex lifestyles and rich secondary metabolite profiles, the genomes of streptomycetes encode a plethora of transcription factors, the vast majority of which are uncharacterized. Herein, we use Surface Plasmon Resonance (SPR) to identify and delineate putative operator sites for SCO3205, a MarR family transcriptional regulator from Streptomyces coelicolor that is well represented in sequenced actinomycete genomes. In particular, we use a novel SPR footprinting approach that exploits indirect ligand capture to vastly extend the lifetime of a standard streptavidin SPR chip. We define two operator sites upstream of sco3205 and a pseudopalindromic consensus sequence derived from these enables further potential operator sites to be identified in the S. coelicolor genome. We evaluate each of these through SPR and test the importance of the conserved bases within the consensus sequence. Informed by these results, we determine the crystal structure of a SCO3205-DNA complex at 2.8 Å resolution, enabling molecular level rationalization of the SPR data. Taken together, our observations support a DNA recognition mechanism involving both direct and indirect sequence readout.

    Organizational Affiliation: 

    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE MARR-FAMILY TRANSCRIPTIONAL REPRESSOR
A, B, E, F
177Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 0 
Find proteins for Q9KYU1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9KYU1
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*GP*AP*TP*TP*GP*AP*GP*AP*TP*CP*TP *CP*AP*AP*TP*CP*TP*TP*DT)-3'C,D,G,H22synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download SDF File 
Download CCD File 
A, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.176 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 70.800α = 90.00
b = 70.800β = 90.00
c = 557.480γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
Aimlessdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2019-02-20
    Type: Data collection, Other, Source and taxonomy