3FT7

Crystal structure of an extremely stable dimeric protein from sulfolobus islandicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.177 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure-Based Stability Analysis of an Extremely Stable Dimeric DNA Binding Protein from Sulfolobus islandicus

Weininger, U.Zeeb, M.Neumann, P.Low, C.Stubbs, M.T.Lipps, G.Balbach, J.

(2009) Biochemistry 48: 10030-10037

  • DOI: https://doi.org/10.1021/bi900760n
  • Primary Citation of Related Structures:  
    2K9I, 3FT7

  • PubMed Abstract: 

    ORF56 is a small and thermodynamically extremely stable dimeric protein from the archaeon Sulfolobus islandicus. This DNA binding protein is encoded on plasmid pRN1 and possibly controls the copy number of the plasmid. We report the solution NMR structure as well as the crystal structure of ORF56 comprising a ribbon-helix-helix fold. The homodimer consists of an antiparallel intersubunit beta-sheet and two alpha-helices per monomer, which is a common DNA binding fold of plasmid- and phage-encoded gene regulation proteins. NMR titration experiments with ORF56 and double-stranded DNA derived from its promoter binding site revealed that it is largely the beta-sheets that interact with the DNA. The beta-sheet experiences high local fluctuations, which are conserved among DNA binding ribbon-helix-helix dimers from mesophilic and hyperthermophilic organisms. In contrast, residues strongly protected against H-D exchange are localized in helix 2, forming the hydrophobic intermolecular core of the dimer. A structure-based comparison of the intermolecular binding surface and the change in accessible surface area upon unfolding of various ribbon-helix-helix dimers with the Gibbs free energy changes and m values show a correlation between hydrophobicity of these surface areas and stability. These findings provide possible explanations for the very high thermodynamic stability of ORF56 with retained DNA binding capacity.


  • Organizational Affiliation

    Institut fur Physik, Biophysik, Martin-Luther-Universitat Halle-Wittenberg, D-06120 Halle (Saale), Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein ORF56
A, B
55Sulfolobus islandicusMutation(s): 0 
Gene Names: PLASMID PRN1
UniProt
Find proteins for Q54323 (Sulfolobus islandicus)
Explore Q54323 
Go to UniProtKB:  Q54323
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54323
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.177 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.03α = 90
b = 33.03β = 90
c = 85.69γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 1.3: 2017-11-01
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-11-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description