8RX4 | pdb_00008rx4

Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD and redox co-factor NADP(H)

PDB DOI: https://doi.org/10.2210/pdb8RX4/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium xenopi
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-02-06 Released: 2025-08-20
Deposition Author(s): Oorts, L., Osipov, E.M., Beelen, S., Strelkov, S.V.
Funding Organization(s): Research Foundation - Flanders (FWO), European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.278 (Depositor), 0.277 (DCC)
R-Value Work:
0.233 (Depositor), 0.233 (DCC)
R-Value Observed:
0.235 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Structure of mycothione reductase

Oorts, L., Osipov, E.M., Beelen, S., Strelkov, S.V.

To be published.

Macromolecule Content

Total Structure Weight: 103.52 kDa
Atom Count: 7,317
Modeled Residue Count: 918
Deposited Residue Count: 918
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mycothione reductase	A, B	459	Mycobacterium xenopi	Mutation(s): 0 Gene Names: mtr, I553_7456 EC: 1.8.1.15
UniProt
Find proteins for P9WHH3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHH3 Go to UniProtKB: P9WHH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WHH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.278 (Depositor), 0.277 (DCC)
R-Value Work: 0.233 (Depositor), 0.233 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.813	α = 90
b = 64.996	β = 100.44
c = 137.536	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	I007220N
Research Foundation - Flanders (FWO)	Belgium	G066619N
European Union (EU)	European Union	853903

Revision History (Full details and data files)

Version 1.0: 2025-08-20
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.