3CMI | pdb_00003cmi

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.256 (Depositor), 0.260 (DCC)
R-Value Work:
0.224 (Depositor), 0.224 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.22220
Primary Citation Related Structures:
3CMI

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40581
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.256 (Depositor), 0.260 (DCC)
R-Value Work: 0.224 (Depositor), 0.224 (DCC)
R-Value Observed: 0.226 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.