3CMI

Crystal structure of glutathione-dependent phospholipid peroxidase Hyr1 from the yeast Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3CMI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-21 Released: 2008-09-16 
• Deposition Author(s): Zhang, W.J.Z., He, Y.X., Yu, J., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 

Starting Model: experimental

Literature

Crystal structure of glutathione-dependent phospholipid peroxidase Hyr1 from the yeast Saccharomyces cerevisiae

Zhang, W.J., He, Y.X., Yang, Z., Yu, J., Chen, Y., Zhou, C.Z.

(2008) Proteins 73: 1058-1062

• PubMed: 18767166 
• DOI: https://doi.org/10.1002/prot.22220
• Primary Citation of Related Structures:  
  3CMI

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 19.68 kDa 
• Atom Count: 1,189 
• Modelled Residue Count: 143 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin HYR1	A	171	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: HYR1, GPX3, ORP1 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for P40581 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40581  Go to UniProtKB:  P40581

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.256 
• R-Value Work: 0.224 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.57	α = 90
b = 64.88	β = 90
c = 72.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Zhang, W.J.Z., He, Y.X., Yu, J., Zhou, C.Z.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description