5YKJ | pdb_00005ykj

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.53 Å
R-Value Free:
0.193 (Depositor), 0.193 (DCC)
R-Value Work:
0.178 (Depositor), 0.179 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

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: 24.27 kDa
Atom Count: 1,946
Modeled Residue Count: 213
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34227
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on 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 (Depositor), 0.193 (DCC)
R-Value Work: 0.178 (Depositor), 0.179 (DCC)
R-Value Observed: 0.179 (Depositor)

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

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