2PN8 | pdb_00002pn8

Crystal structure of human peroxiredoxin 4 (thioredoxin peroxidase)

PDB DOI: https://doi.org/10.2210/pdb2PN8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-04-24 Released: 2007-05-22
Deposition Author(s): Pilka, E.S., Kavanagh, K.L., Cooper, C., von Delft, F., Sundstrom, M., Arrowsmith, C.A., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.185 (Depositor), 0.194 (DCC)
R-Value Work:
0.151 (Depositor), 0.163 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human peroxiredoxin 4 (thioredoxin peroxidase).

Pilka, E.S., Kavanagh, K.L., Cooper, C., von Delft, F., Sundstrom, M., Arrowsmith, C.A., Weigelt, J., Edwards, A., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 240.31 kDa
Atom Count: 17,618
Modeled Residue Count: 1,908
Deposited Residue Count: 2,110
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-4	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	211	Homo sapiens	Mutation(s): 0 Gene Names: PRDX4 EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13162 (Homo sapiens) Explore Q13162 Go to UniProtKB: Q13162
PHAROS: Q13162 GTEx: ENSG00000123131
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13162
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.185 (Depositor), 0.194 (DCC)
R-Value Work: 0.151 (Depositor), 0.163 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.188	α = 90
b = 138.776	β = 104.52
c = 108.989	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-22

Deposition Author(s):

Arrowsmith, C.A.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-05-22
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-30
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.