2DFF

Crystal structure of Tk-RNase HII(1-204)-C

• PDB DOI: https://doi.org/10.2210/pdb2DFF/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus kodakarensis KOD1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-01 Released: 2007-03-06 
• Deposition Author(s): Katagiri, Y., Takano, K., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.299 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 

Starting Model: experimental

Literature

Conformational contagion in a protein: Structural properties of a chameleon sequence

Takano, K., Katagiri, Y., Mukaiyama, A., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

(2007) Proteins 68: 617-625

• PubMed: 17510955 
• DOI: https://doi.org/10.1002/prot.21451
• Primary Citation of Related Structures:  
  2DF5, 2DFE, 2DFF, 2DFH, 2DFI


• PubMed Abstract: 
  

  Certain sequences, known as chameleon sequences, take both alpha- and beta-conformations in natural proteins. We demonstrate that a wild chameleon sequence fused to the C-terminal alpha-helix or beta-sheet in foreign stable proteins from hyperthermophiles forms the same conformation as the host secondary structure. However, no secondary structural formation is observed when the sequence is attached to the outside of the secondary structure. These results indicate that this sequence inherently possesses an ability to make either alpha- or beta-conformation, depending on the sequentially neighboring secondary structure if little other nonlocal interaction occurs. Thus, chameleon sequences take on a satellite state through contagion by the power of a secondary structure. We propose this "conformational contagion" as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases.

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Organizational Affiliation: 

Department of Material and Life Science, Osaka University, Suita, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.96 kDa 
• Atom Count: 1,613 
• Modelled Residue Count: 210 
• Deposited Residue Count: 213 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease HII	A	213	Thermococcus kodakarensis KOD1	Mutation(s): 0  EC: 3.1.26.4
UniProt
Find proteins for O74035 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O74035  Go to UniProtKB:  O74035

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.299 
• R-Value Work: 0.248 
• R-Value Observed: 0.248 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.525	α = 90
b = 67.109	β = 90
c = 52.209	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Katagiri, Y., Takano, K., Chon, H., Matsumura, H., Koga, Y., Kanaya, S.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description