9FYH | pdb_00009fyh

Dye Type Peroxidase Aa from Streptomyces lividans by microcrystal electron diffraction (MicroED/3D ED)

• PDB DOI: https://doi.org/10.2210/pdb9FYH/pdb

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


• Deposited: 2024-07-03 Released: 2025-07-16 
• Deposition Author(s): Hofer, G., Wang, L., Pacoste, L., Hager, P., Finjallaz, A., Williams, L., Worral, J., Steiner, R., Xu, H., Zou, X.
• Funding Organization(s): Knut and Alice Wallenberg Foundation, Swedish Research Council

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Universal Serial electron diffraction for high quality protein structures

Hofer, G., Wang, L., Pacoste, L., Hager, P., Fonjallaz, A., Williams, L., Worrall, J., Steiner, R., Xu, H., Zou, X.

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)

Macromolecule Content 

• Total Structure Weight: 81.71 kDa 
• Atom Count: 5,863 
• Modeled Residue Count: 729 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase	A, B	373	Streptomyces lividans	Mutation(s): 0  Gene Names: SLI_2602
UniProt
Find proteins for A0ABF7PG09 (Streptomyces lividans TK24) Explore A0ABF7PG09  Go to UniProtKB:  A0ABF7PG09

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.77	α = 90
b = 67.4	β = 105.8
c = 73.63	γ = 90

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Hofer, G., Wang, L., Pacoste, L., Hager, P., Finjallaz, A., Williams, L., Worral, J., Steiner, R., Xu, H., Zou, X.

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Funding Organization	Location	Grant Number
Knut and Alice Wallenberg Foundation	Sweden	--
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release