7YZT

Crystal structure of a dye-decolorizing (Dyp) peroxidase from Acinetobacter radioresistens

• PDB DOI: https://doi.org/10.2210/pdb7YZT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acinetobacter radioresistens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-02-21 Released: 2023-01-25 
• Deposition Author(s): Zhang, C., Catucci, G., Gilardi, G., Sadeghi, S.J., Di Nardo, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Crystal structure of a decolorizing peroxidase (Dyp) from Acinetobacter radioresistens

Catucci, G., Zhang, C., Di Nardo, G., Sadeghi, S.J., Gilardi, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 108.89 kDa 
• Atom Count: 8,638 
• Modelled Residue Count: 918 
• Deposited Residue Count: 945 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyp-type peroxidase family protein	A, B, C	315	Acinetobacter radioresistens	Mutation(s): 0  Gene Names: HMPREF0018_02696

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.196 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.14	α = 90
b = 88.14	β = 90
c = 231.569	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Zhang, C., Catucci, G., Gilardi, G., Sadeghi, S.J., Di Nardo, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description