1R71

Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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This is version 1.3 of the entry. See complete history. 


Literature

Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB.

Khare, D., Ziegelin, G., Lanka, E., Heinemann, U.

(2004) Nat Struct Mol Biol 11: 656-663

  • DOI: https://doi.org/10.1038/nsmb773
  • Primary Citation of Related Structures:  
    1R71

  • PubMed Abstract: 

    The KorB protein of the broad-host-range plasmid RP4 acts as a multifunctional regulator of plasmid housekeeping genes, including those responsible for replication, maintenance and conjugation. Additionally, KorB functions as the ParB analog of the plasmid's partitioning system. The protein structure consists of eight helices, two of which belong to a predicted helix-turn-helix motif. Each half-site of the palindromic operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based mainly on two side chain interactions outside the helix-turn-helix motif with two bases next to the central base pair of the 13-base pair operator sequence. The surface of the KorB DNA-binding domain mirrors the overall acidity of KorB, whereas DNA binding occurs via a basic interaction surface. We present a model of KorB, including the structure of its dimerization domain, and discuss its interactions with the highly basic ParA homolog IncC.

    • Organizational Affiliation: 

    Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional repressor protein korBI [auth A],
J [auth B],
K [auth C],
L [auth D]		178Escherichia coliMutation(s): 0 
Gene Names: korB
UniProt
Find proteins for P07674 (Escherichia coli)
Explore P07674 
Go to UniProtKB:  P07674
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07674
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3'A [auth E],
D [auth J],
E [auth G],
H [auth K]		17N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3'B [auth I],
C [auth F],
F [auth L],
G [auth H]		17N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.44α = 90
b = 110.44β = 90
c = 160.53γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling
SOLVEphasing
RESOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description