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

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
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Continuous Serial Electron Diffraction for High Quality Protein Structures

Hofer, G., Wang, L., Pacoste, L., Hager, P., Fonjallaz, A., Williams, L., Scaletti Hutchinson, E., Di Palma, M., Stenmark, P., Worral, J., Steiner, R.A., Xu, H., Zou, X.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.09.14.676192

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deferrochelatase	A, B	373	Streptomyces lividans	Mutation(s): 0 Gene Names: SLI_2602 EC: 1.11.1
UniProt
Find proteins for A0ABF7PG09 (Streptomyces lividans TK24) Explore A0ABF7PG09 Go to UniProtKB: A0ABF7PG09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0ABF7PG09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release
Version 1.1: 2026-01-28
Changes: Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.