Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.07 kDa 
• Atom Count: 918 
• Modelled Residue Count: 110 
• Deposited Residue Count: 110 
• Unique protein chains: 1

2K9I

NMR structure of plasmid copy control protein ORF56 from sulfolobus islandicus

• PDB DOI: 10.2210/pdb2K9I/pdb
• BMRB: 15987

• Classification: DNA BINDING PROTEIN
• Organism(s): Sulfolobus islandicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-15 Released: 2009-10-20 
• Deposition Author(s): Weininger, U., Balbach, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

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

• PubMed: 19788170 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ORF56	A, B	55	Sulfolobus islandicus	Mutation(s): 0
UniProt
Find proteins for Q54323 (Sulfolobus islandicus) Explore Q54323  Go to UniProtKB:  Q54323

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2K9I Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-10-15 
• Released Date: 2009-10-20 
Deposition Author(s): Weininger, U., Balbach, J.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2016-12-14
  Changes: Structure summary