5YKW

Structural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems

• PDB DOI: https://doi.org/10.2210/pdb5YKW/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-10-16 Released: 2018-10-24 
• Deposition Author(s): Li, C.C., Yang, J., Yang, M.J., Liu, L., Peng, C.T., Li, T., He, L.H., Song, Y.J., Zhu, Y.B., Zhao, N.L., Zhao, C., Bao, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.210 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Structural basis of the thiol resolving mechanism in yeast mitochondrial 1-Cys peroxiredoxin via glutathione/thioredoxin systems

Li, C.C., Yang, J., Yang, M.J., Liu, L., Peng, C.T., Li, T., He, L.H., Song, Y.J., Zhu, Y.B., Zhao, N.L., Zhao, C., Bao, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 12.68 kDa 
• Atom Count: 914 
• Modelled Residue Count: 114 
• Deposited Residue Count: 114 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-3, mitochondrial	A	106	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: TRX3, YCR083W, YCR83W
UniProt
Find proteins for P25372 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25372  Go to UniProtKB:  P25372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide THR-PRO-VAL-CYS-THR-THR-GLU-VAL	B	8	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRX1 EC: 1.11.1.27 (UniProt), 1.11.1.25 (UniProt)
UniProt
Find proteins for P34227 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34227  Go to UniProtKB:  P34227

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.210 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.333	α = 90
b = 49.333	β = 90
c = 50.612	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Li, C.C., Yang, J., Yang, M.J., Liu, L., Peng, C.T., Li, T., He, L.H., Song, Y.J., Zhu, Y.B., Zhao, N.L., Zhao, C., Bao, R.

Revision History  

• Version 1.0: 2018-10-24
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary