9FBC | pdb_00009fbc

Dye-decolourising peroxidase DtpB (448 kGy)

• PDB DOI: https://doi.org/10.2210/pdb9FBC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces lividans 1326
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-13 Released: 2025-05-28 
• Deposition Author(s): Lucic, M., Worrall, J.A.R., Hough, M.A., Strange, R.W., Owen, R.L.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 
  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Dye-decolourising peroxidase DtpB (448 kGy)

Lucic, M., Worrall, J.A.R., Hough, M.A., Strange, R.W., Owen, R.L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 206.78 kDa 
• Atom Count: 14,026 
• Modeled Residue Count: 1,833 
• Deposited Residue Count: 1,878 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup	A, B, C, D, E, F	313	Streptomyces lividans 1326	Mutation(s): 0  Gene Names: SLI_7409
UniProt
Find proteins for A0A7U9HFU5 (Streptomyces lividans 1326) Explore A0A7U9HFU5  Go to UniProtKB:  A0A7U9HFU5

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free:  0.286 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.984	α = 90
b = 121.963	β = 90
c = 199.607	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Lucic, M., Worrall, J.A.R., Hough, M.A., Strange, R.W., Owen, R.L.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	--

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release