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- PDB-8rx6: Mycothione reductase from Mycobacterium tuberculosis in complex w... -

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Basic information

Entry
Database: PDB / ID: 8rx6
TitleMycothione reductase from Mycobacterium tuberculosis in complex with Respiri-1093
ComponentsMycothione reductase
KeywordsOXIDOREDUCTASE / Complex Oxidoreductase NADPH dependent Flavoprotein
Function / homology
Function and homology information


Mycothiol metabolism / mycothione reductase / mycothione reductase [NAD(P)H] activity / mycothiol metabolic process / dihydrolipoyl dehydrogenase (NADH) activity / 2-oxoglutarate metabolic process / pyruvate metabolic process / NADPH binding / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Mycothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / Mycothione reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsOorts, L. / Osipov, E.M. / Beelen, S. / Strelkov, S.V.
Funding support Belgium, European Union, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)I007220N Belgium
Research Foundation - Flanders (FWO)G066619N Belgium
European Union (EU)853903European Union
CitationJournal: To Be Published
Title: Structure of mycothione reductase
Authors: Oorts, L. / Osipov, E.M. / Beelen, S. / Strelkov, S.V.
History
DepositionFeb 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mycothione reductase
B: Mycothione reductase
C: Mycothione reductase
D: Mycothione reductase
E: Mycothione reductase
F: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,48414
Polymers300,0096
Non-polymers5,4748
Water543
1
A: Mycothione reductase
B: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5744
Polymers100,0032
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-57 kcal/mol
Surface area35280 Å2
MethodPISA
2
C: Mycothione reductase
D: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9555
Polymers100,0032
Non-polymers1,9523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-55 kcal/mol
Surface area35560 Å2
MethodPISA
3
E: Mycothione reductase
F: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9555
Polymers100,0032
Non-polymers1,9523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-52 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.757, 175.757, 261.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein
Mycothione reductase / Mycothiol-disulfide reductase / NADPH-dependent mycothione reductase


Mass: 50001.574 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mtr, gorA, Rv2855 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P9WHH3, mycothione reductase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-A1H3R / (3~{S})-4-[4-(1-benzothiophen-3-yl)-6,7,8,9-tetrahydro-5~{H}-pyrimido[4,5-d]azepin-2-yl]-3-methyl-morpholine / Respiri-1093


Mass: 380.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24N4OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.48 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, sodium chloride, bis-tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967697 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967697 Å / Relative weight: 1
ReflectionResolution: 3.42→112.26 Å / Num. obs: 56242 / % possible obs: 100 % / Redundancy: 9 % / CC1/2: 0.976 / Rmerge(I) obs: 0.572 / Rpim(I) all: 0.204 / Rrim(I) all: 0.608 / Χ2: 0.96 / Net I/σ(I): 5.2 / Num. measured all: 508699
Reflection shellResolution: 3.42→3.6 Å / % possible obs: 100 % / Redundancy: 8.9 % / Rmerge(I) obs: 3.432 / Num. measured all: 71897 / Num. unique obs: 8090 / CC1/2: 0.597 / Rpim(I) all: 1.228 / Rrim(I) all: 3.649 / Χ2: 0.94 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→112.26 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2699 2784 5.01 %
Rwork0.2331 --
obs0.2349 55609 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.42→112.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21054 0 372 3 21429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221842
X-RAY DIFFRACTIONf_angle_d0.4729750
X-RAY DIFFRACTIONf_dihedral_angle_d7.8833136
X-RAY DIFFRACTIONf_chiral_restr0.0433398
X-RAY DIFFRACTIONf_plane_restr0.0033846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.480.35741260.31882495X-RAY DIFFRACTION95
3.48-3.540.35271280.31822589X-RAY DIFFRACTION97
3.54-3.610.35151380.30412544X-RAY DIFFRACTION98
3.61-3.680.32111290.29022600X-RAY DIFFRACTION99
3.68-3.760.30291420.27522580X-RAY DIFFRACTION99
3.76-3.850.32231260.27542606X-RAY DIFFRACTION99
3.85-3.940.30541390.27242605X-RAY DIFFRACTION99
3.95-4.050.32871430.2582609X-RAY DIFFRACTION99
4.05-4.170.25881340.23092626X-RAY DIFFRACTION99
4.17-4.310.2481440.22012636X-RAY DIFFRACTION99
4.31-4.460.2551500.212622X-RAY DIFFRACTION100
4.46-4.640.22781360.20032659X-RAY DIFFRACTION100
4.64-4.850.22331410.19322657X-RAY DIFFRACTION100
4.85-5.10.28071120.19132678X-RAY DIFFRACTION100
5.1-5.420.24441350.20912681X-RAY DIFFRACTION100
5.42-5.840.27071520.2232679X-RAY DIFFRACTION100
5.84-6.430.26651400.22732679X-RAY DIFFRACTION100
6.43-7.360.28751550.23322707X-RAY DIFFRACTION100
7.36-9.270.21251550.18952745X-RAY DIFFRACTION100
9.27-112.260.22311590.21632828X-RAY DIFFRACTION97

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