1CA5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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.Biol. 303: 395-403

  • DOI: 10.1006/jmbi.2000.4112
  • Primary Citation of Related Structures:  1C8C, 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 de ...

    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.


    Related Citations: 
    • 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.-J.
      (1998) Nature 392: 202
    • The Crystal Structure of the Hyperthermophile Chromosomal Protein Sso7D Bound to DNA
      Gao, Y.-G.,Su, S.,Robinson, H.,Padmanabhan, S.,Lim, L.,McCrary, B.S.,Edmondson, S.P.,Shriver, J.W.,Wang, A.H.-J.
      (1998) Nat.Struct.Mol.Biol. 5: 782


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CHROMOSOMAL PROTEIN SAC7D
A
66Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)N/A
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  P13123
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3'B,C8N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.780α = 90.00
b = 76.760β = 90.00
c = 35.140γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-23
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-28
    Type: Advisory
  • Version 1.4: 2017-10-04
    Type: Refinement description