1BNZ

SSO7D HYPERTHERMOPHILE PROTEIN/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1BNZ/pdb
• BMRB: 5909
• BMRB: 5910
• NAKB: 1BNZ

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Sulfolobus acidocaldarius
• Mutation(s): No 


• Deposited: 1998-07-31 Released: 1998-11-11 
• Deposition Author(s): Gao, Y.-G., Su, S.-Y., Robinson, H., Padmanabhan, S., Lim, L., Mccrary, B.S., Edmondos, S.P., Shrive, J.W., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 

Literature

The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.

Gao, Y.G., Su, S.Y., Robinson, H., Padmanabhan, S., Lim, L., McCrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.

(1998) Nat Struct Biol 5: 782-786

• PubMed: 9731772 
• DOI: https://doi.org/10.1038/1822
• Primary Citation of Related Structures:  
  1BF4, 1BNZ


• PubMed Abstract: 
  

  Sso7d and Sac7d are two small (approximately 7,000 Mr), but abundant, chromosomal proteins from the hyperthermophilic archaeabacteria Sulfolobus solfataricus and S. acidocaldarius respectively. These proteins have high thermal, acid and chemical stability. They bind DNA without marked sequence preference and increase the Tm of DNA by approximately 40 degrees C. Sso7d in complex with GTAATTAC and GCGT(iU)CGC + GCGAACGC was crystallized in different crystal lattices and the crystal structures were solved at high resolution. Sso7d binds in the minor groove of DNA and causes a single-step sharp kink in DNA (approximately 60 degrees) by the intercalation of the hydrophobic side chains of Val 26 and Met 29. The intercalation sites are different in the two complexes. Observations of this novel DNA binding mode in three independent crystal lattices indicate that it is not a function of crystal packing.

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Organizational Affiliation: 

Department of Cell and Structural Biology, University of Illinois at Urbana-Champaign, Urbana 61801, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.15 kDa 
• Atom Count: 931 
• Modelled Residue Count: 80 
• Deposited Residue Count: 80 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-BINDING PROTEIN 7A	C [auth A]	64	Sulfolobus acidocaldarius	Mutation(s): 0
UniProt
Find proteins for P39476 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P39476  Go to UniProtKB:  P39476

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3'	A [auth B], B [auth C]	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.6	α = 90
b = 50.77	β = 90
c = 42.06	γ = 90

Software Package:

Software Name	Purpose
PHASIT	model building
X-PLOR	refinement
PHASIT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-11 
Deposition Author(s): Gao, Y.-G., Su, S.-Y., Robinson, H., Padmanabhan, S., Lim, L., Mccrary, B.S., Edmondos, S.P., Shrive, J.W., Wang, A.H.-J.

Revision History  

• Version 1.0: 1998-11-11
  Type: Initial release
  
• Version 1.1: 2011-05-09
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Other
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references