9Q5L | pdb_00009q5l

Cryo-EM structure of a Paracoccus Trimethylamine N-oxide Demethylase in complex with DMA, HCHO

PDB DOI: https://doi.org/10.2210/pdb9Q5L/pdb
EM Map EMD-72239: EMDB EMDataResource

Classification: METAL BINDING PROTEIN
Organism(s): Paracoccus sp. DMF
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-08-20 Released: 2026-08-26
Deposition Author(s): Thach, T., Subramanian, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Q5L

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

Literature

Bifunctional Architecture Enables Substrate Catalysis and Channeling in Paracoccus TMAO Demethylase

Thach, T., Dhanabalan, K., Maurya, S., Han-Hallet, Y., Quan, S., Allison, J., Ramanathan, G., Subramanian, R.

(2026) Elife

DOI: https://doi.org/10.7554/elife.109964.2

Macromolecule Content

Total Structure Weight: 348.29 kDa
Atom Count: 16,468
Modeled Residue Count: 2,130
Deposited Residue Count: 3,172
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
trimethylamine N-oxide demethylase	A, B, C, D	793	Paracoccus sp. DMF	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
DMN (Subject of Investigation/LOI) Query on DMN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	DIMETHYLAMINE C₂ H₇ N ROSDSFDQCJNGOL-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
FOR (Subject of Investigation/LOI) Query on FOR Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	FORMYL GROUP C H₂ O WSFSSNUMVMOOMR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Subramanian, R.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

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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.