1CA6 | pdb_00001ca6

INTERCALATION SITE OF HYPERTHERMOPHILE CHROMOSOMAL PROTEIN SSO7D/SAC7D BOUND TO DNA

• PDB DOI: https://doi.org/10.2210/pdb1CA6/pdb
• BMRB: 5905
• BMRB: 5910
• BMRB: 5908
• BMRB: 5909
• NAKB: 1CA6

• Classification: STRUCTURAL PROTEIN/DNA
• Organism(s): synthetic construct, Sulfolobus acidocaldarius
• Mutation(s): No 


• Deposited: 1999-02-23 Released: 2000-02-23 
• Deposition Author(s): Su, S., Gao, Y.-G., Robinson, H., Shriver, J.W., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.257 (Depositor) 
• R-Value Work: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs

Su, S., Gao, Y.-G., Robinson, H., Liaw, Y.C., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

(2000) J Mol Biology 303: 395-403

• PubMed: 11031116 
• DOI: https://doi.org/10.1006/jmbi.2000.4112
• Primary Citation Related Structures: 
  1C8C, 1CA5, 1CA6


• PubMed Abstract: 
  

  Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation.

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Organizational Affiliation: 
• Center for Biophysics and COmputational BIology, University of Illinois at Urbana-Champaign, 61801, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.51 kDa 
• Atom Count: 929 
• Modeled 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
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
5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3'	A [auth B], B [auth C]	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.257 (Depositor) 
• R-Value Work:  0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.47	α = 90
b = 75.89	β = 90
c = 35	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-23 
Deposition Author(s): Su, S., Gao, Y.-G., Robinson, H., Shriver, J.W., Wang, A.H.-J.

Revision History  

• Version 1.0: 2000-02-23
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-12-28
  Changes: Advisory
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2019-11-06
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.6: 2023-08-09
  Changes: Data collection, Database references, Refinement description