2YWN

Crystal structure of peroxiredoxin-like protein from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb2YWN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-20 Released: 2007-10-23 
• Deposition Author(s): Ebihara, A., Manzoku, M., Fujimoto, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4G2E

Literature

Crystal structure of peroxiredoxin-like protein from Sulfolobus tokodaii

Ebihara, A., Manzoku, M., Fujimoto, Y., Yokoyama, S., Kuramitsu, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.82 kDa 
• Atom Count: 1,360 
• Modelled Residue Count: 150 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-like protein	A	157	Sulfurisphaera tokodaii	Mutation(s): 0
UniProt
Find proteins for F9VNL8 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VNL8  Go to UniProtKB:  F9VNL8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.34	α = 90
b = 78.67	β = 90
c = 61.97	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-23 
Deposition Author(s): Ebihara, A., Manzoku, M., Fujimoto, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description