5YKJ

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

• PDB DOI: https://doi.org/10.2210/pdb5YKJ/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-14 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: 1.53 Å
• R-Value Free: 0.193 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

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: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.27 kDa 
• Atom Count: 1,946 
• Modelled Residue Count: 213 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin PRX1, mitochondrial	A	214	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PRX1, YBL064C, YBL0503, YBL0524 EC: 1.11.1.15 (PDB Primary Data), 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.193 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.03	α = 90
b = 84.03	β = 90
c = 62.784	γ = 90

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: 2024-10-16
  Changes: Data collection, Database references, Structure summary