Biological Assembly 1  

 3D View: Structure | Electron Density

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.48 kDa 
• Atom Count: 987 
• Residue Count: 82 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1AZP

HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SAC7D BOUND WITH KINKED DNA DUPLEX

• DOI: 10.2210/pdb1AZP/pdb
• BMRB: 5908
• NDB: PDR047

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


• Deposited: 1997-11-19 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.252 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 

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: 10.1038/32455
• Structures With Same Primary Citation


• 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.

---

Organizational Affiliation: 

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

Macromolecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.252 
• R-Value Work: 0.211 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.108	α = 90
b = 77.173	β = 90
c = 35.48	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
BIOTEX	data reduction
BIOTEX	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-11-19 
• 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