9FBZ | pdb_00009fbz

Dye-decolourising peroxidase DtpB mixed with hydrogen peroxide for 1.3 s

PDB DOI: https://doi.org/10.2210/pdb9FBZ/pdb

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

Deposited: 2024-05-15 Released: 2025-05-28
Deposition Author(s): Lucic, M., Worrall, J.A.R., Hough, M.A., Owen, R.L., Devenish, N.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.198 (Depositor), 0.198 (DCC)
R-Value Work:
0.167 (Depositor), 0.172 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Dye-decolourising peroxidase DtpB mixed with hydrogen peroxide for 1.3 s

Lucic, M., Worrall, J.A.R., Hough, M.A., Owen, R.L., Devenish, N.

To be published.

Macromolecule Content

Total Structure Weight: 206.89 kDa
Atom Count: 15,076
Modeled Residue Count: 1,833
Deposited Residue Count: 1,878
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dye-decolorizing peroxidase (DyP), encapsulated subgroup	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7U9HFU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F]	G [auth A] J [auth B] K [auth C] M [auth D] O [auth E] G [auth A], J [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth C] mmCIF format, chain H [auth A] mmCIF format, chain L [auth C]	H [auth A], L [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth C]
O (Subject of Investigation/LOI) Query on O Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] MOL2 format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] mmCIF format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F]	I [auth A], N [auth D], P [auth E], R [auth F]	OXYGEN ATOM O XLYOFNOQVPJJNP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain I [auth A] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]