1AZQ

HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX

• PDB DOI: https://doi.org/10.2210/pdb1AZQ/pdb
• BMRB: 5905
• BMRB: 5908
• NAKB: 1AZQ

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


• Deposited: 1997-11-20 Released: 1999-01-13 
• Deposition Author(s): Robinson, H., Gao, Y.-G., Mccrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.238 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 

Starting Model: experimental

Literature

The hyperthermophile chromosomal protein Sac7d sharply kinks DNA.

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

(1998) Nature 392: 202-205

• PubMed: 9515968 
• DOI: https://doi.org/10.1038/32455
• Primary Citation of Related Structures:  
  1AZP, 1AZQ


• PubMed Abstract: 
  

  The proteins Sac7d and Sso7d belong to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius and S. solfactaricus, respectively. These proteins are extremely stable to heat, acid and chemical agents. Sac7d binds to DNA without any particular sequence preference and thereby increases its melting temperature by approximately 40 degrees C. We have now solved and refined the crystal structure of Sac7d in complex with two DNA sequences to high resolution. The structures are examples of a nonspecific DNA-binding protein bound to DNA, and reveal that Sac7d binds in the minor groove, causing a sharp kinking of the DNA helix that is more marked than that induced by any sequence-specific DNA-binding proteins. The kink results from the intercalation of specific hydrophobic side chains of Sac7d into the DNA structure, but without causing any significant distortion of the protein structure relative to the uncomplexed protein in solution.

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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: 12.48 kDa 
• Atom Count: 923 
• Modelled Residue Count: 82 
• Deposited Residue Count: 82 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D)	C [auth A]	66	Sulfolobus acidocaldarius	Mutation(s): 0
UniProt
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore P13123  Go to UniProtKB:  P13123

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (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: 1.94 Å
• R-Value Free: 0.238 
• R-Value Work: 0.186 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.765	α = 90
b = 77.528	β = 90
c = 36.542	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Robinson, H., Gao, Y.-G., Mccrary, B.S., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Refinement description