5YKW | pdb_00005ykw

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.210 (Depositor), 0.209 (DCC)
R-Value Work:
0.175 (Depositor), 0.182 (DCC)
R-Value Observed:
0.178 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5YKW

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25372
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
UniProt Group	P34227
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.210 (Depositor), 0.209 (DCC)
R-Value Work: 0.175 (Depositor), 0.182 (DCC)
R-Value Observed: 0.178 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Revision History (Full details and data files)

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

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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.