8PXP | pdb_00008pxp

Compound II structure of Y389F variant of A type dye-decolourising peroxidase DtpAa

• PDB DOI: https://doi.org/10.2210/pdb8PXP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces lividans 1326
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-07-24 Released: 2024-08-07 
• Deposition Author(s): Lucic, M., Thompson, A., Worrall, J.A.R., Hough, M.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.250 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Compound II structure of A type dye-decolourising peroxidase DtpAa

Lucic, M., Thompson, A., Worrall, J.A.R., Hough, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 89.73 kDa 
• Atom Count: 5,875 
• Modeled Residue Count: 725 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase	A, B	417	Streptomyces lividans 1326	Mutation(s): 1  Gene Names: SLI_2602 EC: 1.11.1
UniProt
Find proteins for A0A7U9DT46 (Streptomyces lividans 1326) Explore A0A7U9DT46  Go to UniProtKB:  A0A7U9DT46

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.250 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.939	α = 90
b = 67.543	β = 104.77
c = 70.797	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2.multiplex	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Lucic, M., Thompson, A., Worrall, J.A.R., Hough, M.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R021015/1

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release