9SWG | pdb_00009swg

Crystal structure of PpDyP E209A variant in complex with manganese

PDB DOI: https://doi.org/10.2210/pdb9SWG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-10-06 Released: 2026-10-21
Deposition Author(s): Borges, P.T., Lorena, C., Martins, L.O.
Funding Organization(s): Foundation for Science and Technology (FCT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.264 (Depositor), 0.268 (DCC)
R-Value Work:
0.219 (Depositor), 0.223 (DCC)
R-Value Observed:
0.221 (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

Crystal structure of PpDyP E209A variant in complex with manganese

Borges, P.T., Lorena, C., Martins, L.O.

To be published.

Macromolecule Content

Total Structure Weight: 188.68 kDa
Atom Count: 13,170
Modeled Residue Count: 1,678
Deposited Residue Count: 1,698
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dyp-type peroxidase family protein	A, B, C, D, E A, B, C, D, E, F	283	Pseudomonas putida	Mutation(s): 1 Gene Names: PP_3248
UniProt
Find proteins for Q88HV5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88HV5 Go to UniProtKB: Q88HV5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88HV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain G [auth A]	G [auth A] I [auth B] K [auth C] L [auth D] M [auth E] G [auth A], I [auth B], K [auth C], L [auth D], M [auth E], N [auth F]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]