5JLY | pdb_00005jly

Structure of Peroxiredoxin-1 from Schistosoma japonicum

• PDB DOI: https://doi.org/10.2210/pdb5JLY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Schistosoma japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-27 Released: 2017-05-03 
• Deposition Author(s): Wu, Q., Huang, F., Zeng, D., Liu, X., Zhao, J., Wang, H., Peng, Y., Li, P., Li, Y.
• Funding Organization(s): National Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.219 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Peroxiredoxin-1 from Schistosoma japonicum

Li, P., Li, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.73 kDa 
• Atom Count: 3,957 
• Modeled Residue Count: 500 
• Deposited Residue Count: 570 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin peroxidase-1	A, B, C	190	Schistosoma japonicum	Mutation(s): 0  Gene Names: SjTPx-1 EC: 1.11.1.24
UniProt
Find proteins for Q75UG3 (Schistosoma japonicum) Explore Q75UG3  Go to UniProtKB:  Q75UG3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.219 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.734	α = 90
b = 199.019	β = 90
c = 70.775	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Wu, Q., Huang, F., Zeng, D., Liu, X., Zhao, J., Wang, H., Peng, Y., Li, P., Li, Y.

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Funding Organization	Location	Grant Number
National Science Foundation of China	China	31260206

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description