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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin-4	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.160 (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

Entry History 

Deposition Data

• Released Date: 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)

Revision History  

• 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