3ALY | pdb_00003aly

Crystal Structure of RNase HI from Sulfolobus tokodaii with C-terminal deletion

• PDB DOI: https://doi.org/10.2210/pdb3ALY/pdb

• Classification: HYDROLASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-10 Released: 2011-06-22 
• Deposition Author(s): Angkawidjaja, C., Takano, K., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.250 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.197 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Stabilization by fusion to the C-terminus of hyperthermophile Sulfolobus tokodaii RNase HI: a possibility of protein stabilization tag

Takano, K., Okamoto, T., Okada, J., Tanaka, S., Angkawidjaja, C., Koga, Y., Kanaya, S.

(2011) PLoS One 6: e16226-e16226

• PubMed: 21283826 
• DOI: https://doi.org/10.1371/journal.pone.0016226
• Primary Citation Related Structures: 
  3ALY


• PubMed Abstract: 
  

  RNase HI from the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) is stabilized by its C-terminal residues. In this work, the stabilization effect of the Sto-RNase HI C-terminal residues was investigated in detail by thermodynamic measurements of the stability of variants lacking the disulfide bond (C58/145A), or the six C-terminal residues (ΔC6) and by structural analysis of ΔC6. The results showed that the C-terminal does not affect overall structure and stabilization is caused by local interactions of the C-terminal, suggesting that the C-terminal residues could be used as a "stabilization tag." The Sto-RNase HI C-terminal residues (-IGCIILT) were introduced as a tag on three proteins. Each chimeric protein was more stable than its wild-type protein. These results suggested the possibility of a simple stabilization technique using a stabilization tag such as Sto-RNase HI C-terminal residues.

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Organizational Affiliation: 
• Department of Material and Life Science, Osaka University, Osaka, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.47 kDa 
• Atom Count: 2,498 
• Modeled Residue Count: 282 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein ST0753	A, B	143	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  Gene Names: ST0753 EC: 3.1.26.4
UniProt
Find proteins for F9VN79 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VN79  Go to UniProtKB:  F9VN79

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.250 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.197 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.975	α = 89.72
b = 41.018	β = 89.71
c = 43.534	γ = 86.76

Software Package:

Software Name	Purpose
BL38	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Angkawidjaja, C., Takano, K., Kanaya, S.

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description