3QPM | pdb_00003qpm

Crystal structure of peroxiredoxin Prx4 from Pseudosciaena crocea

• PDB DOI: https://doi.org/10.2210/pdb3QPM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Larimichthys crocea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-14 Released: 2012-02-22 
• Deposition Author(s): Lian, F.M., Teng, Y.B., Jiang, Y.L., He, Y.X., Chen, Y., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

The N-terminal beta-sheet of peroxiredoxin Prx4 in the large yellow croaker Pseudosciaena crocea is critical for its peroxidase and anti-bacterial activities

Lian, F.M., Mu, Y.N., Teng, Y.B., Ao, J.Q., Jiang, Y.L., He, Y.X., Chen, Y.X., Zhou, C.Z., Chen, X.H.

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: 136.44 kDa 
• Atom Count: 8,438 
• Modeled Residue Count: 974 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxiredoxin	A, B, C, D, E	240	Larimichthys crocea	Mutation(s): 0  EC: 1.11.1.15 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for H3JQV8 (Larimichthys crocea) Explore H3JQV8  Go to UniProtKB:  H3JQV8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.121	α = 90
b = 195.998	β = 105.23
c = 51.74	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Lian, F.M., Teng, Y.B., Jiang, Y.L., He, Y.X., Chen, Y., Zhou, C.Z.

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2026-02-11
  Changes: Advisory, Derived calculations, Structure summary