1UDV | pdb_00001udv

Crystal structure of the hyperthermophilic archaeal dna-binding protein Sso10b2 at 1.85 A

• PDB DOI: https://doi.org/10.2210/pdb1UDV/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-05-07 Released: 2003-08-05 
• Deposition Author(s): Chou, C.-C., Lin, T.-W., Chen, C.-Y., Wang, A.H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms

Chou, C.C., Lin, T.W., Chen, C.Y., Wang, A.H.J.

(2003) J Bacteriol 185: 4066-4073

• PubMed: 12837780 
• DOI: https://doi.org/10.1128/JB.185.14.4066-4073.2003
• Primary Citation Related Structures: 
  1UDV


• PubMed Abstract: 
  

  The crystal structure of a small, basic DNA binding protein, Sso10b2, from the thermoacidophilic archaeon Sulfolobus solfataricus was determined by the Zn multiwavelength anomalous diffraction method and refined to 1.85 A resolution. The 89-amino-acid protein adopts a betaalphabetaalphabetabeta topology. The structure is similar to that of Sso10b1 (also called Alba) from the same organism. However, Sso10b2 contains an arginine-rich loop RDRRR motif, which may play an important role in nucleic acid binding. There are two independent Sso10b2 proteins in the asymmetric unit, and a plausible stable dimer could be deduced from the crystal structure. Topology comparison revealed that Sso10b2 is similar to several RNA-binding proteins, including IF3-C, YhhP, and DNase I. Models of the Sso10b2 dimer bound to either B-DNA or A-DNA have been constructed.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.58 kDa 
• Atom Count: 1,559 
• Modeled Residue Count: 174 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA binding protein SSO10b	A, B	89	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: SSO6877
UniProt
Find proteins for Q97ZF4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97ZF4  Go to UniProtKB:  Q97ZF4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.02	α = 90
b = 134.98	β = 90
c = 35.86	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-05 
Deposition Author(s): Chou, C.-C., Lin, T.-W., Chen, C.-Y., Wang, A.H.J.

Revision History  

• Version 1.0: 2003-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations