1C8C | pdb_00001c8c

CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS

• PDB DOI: https://doi.org/10.2210/pdb1C8C/pdb
• BMRB: 5905
• BMRB: 5910
• BMRB: 5908
• BMRB: 5909
• NAKB: 1C8C

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Saccharolobus solfataricus
• Mutation(s): No 


• Deposited: 2000-05-04 Released: 2001-05-04 
• Deposition Author(s): Su, S., Gao, Y.-G., Robinson, H., Liaw, Y.-C., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.287 (Depositor) 
• R-Value Work: 
  0.235 (DCC) 
• R-Value Observed: 
  0.229 (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.

(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: 12.12 kDa 
• Atom Count: 987 
• Modeled 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	Saccharolobus solfataricus	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*GP*AP*TP*CP*GP*C)-3'	A [auth B], B [auth C]	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.287 (Depositor) 
• R-Value Work:  0.235 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.475	α = 90
b = 49.8	β = 90
c = 37.681	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-04 
Deposition Author(s): Su, S., Gao, Y.-G., Robinson, H., Liaw, Y.-C., Edmondson, S.P., Shriver, J.W., Wang, A.H.-J.

Revision History  

• Version 1.0: 2001-05-04
  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: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Refinement description