2IHF | pdb_00002ihf

Crystal structure of deletion mutant delta 228-252 R190A of the single-stranded DNA binding protein from Thermus aquaticus

• PDB DOI: https://doi.org/10.2210/pdb2IHF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermus aquaticus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-26 Released: 2007-01-02 
• Deposition Author(s): Fedorov, R., Witte, G., Urbanke, C., Manstein, D.J., Curth, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

3D structure of Thermus aquaticus single-stranded DNA-binding protein gives insight into the functioning of SSB proteins.

Fedorov, R., Witte, G., Urbanke, C., Manstein, D.J., Curth, U.

(2006) Nucleic Acids Res 34: 6708-6717

• PubMed: 17148487 
• DOI: https://doi.org/10.1093/nar/gkl1002
• Primary Citation Related Structures: 
  2IHE, 2IHF


• PubMed Abstract: 
  

  In contrast to the majority of tetrameric SSB proteins, the recently discovered SSB proteins from the Thermus/Deinoccus group form dimers. We solved the crystal structures of the SSB protein from Thermus aquaticus (TaqSSB) and a deletion mutant of the protein and show the structure of their ssDNA binding domains to be similar to the structure of tetrameric SSBs. Two conformations accompanied by proline cis-trans isomerization are observed in the flexible C-terminal region. For the first time, we were able to trace 6 out of 10 amino acids at the C-terminus of an SSB protein. This highly conserved region is essential for interaction with other proteins and we show it to adopt an extended conformation devoid of secondary structure. A model for binding this region to the chi subunit of DNA polymerase III is proposed. It explains at a molecular level the reason for the ssb113 phenotype observed in Escherichia coli.

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Organizational Affiliation: 
• Institute for Biophysical Chemistry, Hannover Medical Schoo,l Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 27.58 kDa 
• Atom Count: 1,824 
• Modeled Residue Count: 205 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	A	239	Thermus aquaticus	Mutation(s): 1  Gene Names: ssb
UniProt
Find proteins for Q9KH06 (Thermus aquaticus) Explore Q9KH06  Go to UniProtKB:  Q9KH06

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.633	α = 90
b = 80.423	β = 90
c = 97.783	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-02 
Deposition Author(s): Fedorov, R., Witte, G., Urbanke, C., Manstein, D.J., Curth, U.

Revision History  

• Version 1.0: 2007-01-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description