2A4V | pdb_00002a4v

Crystal Structure of a truncated mutant of yeast nuclear thiol peroxidase

PDB DOI: https://doi.org/10.2210/pdb2A4V/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-06-29 Released: 2006-03-14
Deposition Author(s): Choi, J., Choi, S., Chon, J.-K., Choi, J., Cha, M.-K., Kim, I.-H., Shin, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.215 (Depositor), 0.213 (DCC)
R-Value Work:
0.165 (Depositor), 0.165 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2A4V

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of the C107S/C112S mutant of yeast nuclear 2-Cys peroxiredoxin

Choi, J., Choi, S., Chon, J.-K., Choi, J., Cha, M.-K., Kim, I.-H., Shin, W.

(2005) Proteins 61: 1146-1149

PubMed: 16245326 Search on PubMed
DOI: https://doi.org/10.1002/prot.20704
Primary Citation Related Structures:
2A4V

Organizational Affiliation

Department of Chemistry, Seoul National University, Seoul, Korea.

Macromolecule Content

Total Structure Weight: 17.86 kDa
Atom Count: 1,395
Modeled Residue Count: 156
Deposited Residue Count: 159
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin DOT5	A	159	Saccharomyces cerevisiae	Mutation(s): 3 Gene Names: DOT5 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for P40553 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40553 Go to UniProtKB: P40553
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40553
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.215 (Depositor), 0.213 (DCC)
R-Value Work: 0.165 (Depositor), 0.165 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.535	α = 90
b = 37.535	β = 90
c = 83.256	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-11-10
Changes: Database references
Version 1.5: 2024-05-29
Changes: Data collection

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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.