2A4V

Crystal Structure of a truncated mutant of yeast nuclear thiol peroxidase

• PDB DOI: https://doi.org/10.2210/pdb2A4V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-06-29 Released: 2006-03-14 
• Deposition Author(s): Choi, J., Choi, S., Chon, J.-K., Choi, J., Cha, M.-K., Kim, I.-H., Shin, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin

Choi, J., Choi, S., Chon, J.-K., Choi, J., Cha, M.-K., Kim, I.-H., Shin, W.

(2005) Proteins 61: 1146-1149

• PubMed: 16245326 
• DOI: https://doi.org/10.1002/prot.20704
• Primary Citation of Related Structures:  
  2A4V

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Organizational Affiliation: 

Department of Chemistry, Seoul National University, Seoul, Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.86 kDa 
• Atom Count: 1,395 
• Modelled Residue Count: 156 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin DOT5	A	159	Saccharomyces cerevisiae	Mutation(s): 3  Gene Names: DOT5 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for P40553 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40553  Go to UniProtKB:  P40553

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.535	α = 90
b = 37.535	β = 90
c = 83.256	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Choi, J., Choi, S., Chon, J.-K., Choi, J., Cha, M.-K., Kim, I.-H., Shin, W.

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-11-10
  Changes: Database references
• Version 1.5: 2024-05-29
  Changes: Data collection