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- PDB-8rx4: Mycothione reductase from Mycobacterium xenopi in complex with co... -

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Basic information

Entry
Database: PDB / ID: 8rx4
TitleMycothione reductase from Mycobacterium xenopi in complex with co-factor FAD and redox co-factor NADP(H)
ComponentsMycothione reductase
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE NADPH DEPENDENT FLAVOPROTEIN MYCOTHIONE
Function / homology
Function and homology information


mycothione reductase / mycothione reductase [NAD(P)H] activity / dihydrolipoyl dehydrogenase (NADH) activity / 2-oxoglutarate metabolic process / flavin adenine dinucleotide binding
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Mycothione reductase
Similarity search - Component
Biological speciesMycobacterium xenopi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 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

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Assembly

Deposited unit
A: Mycothione reductase
B: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5166
Polymers100,4582
Non-polymers3,0584
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12520 Å2
ΔGint-61 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.813, 64.996, 137.536
Angle α, β, γ (deg.)90.00, 100.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mycothione reductase


Mass: 50228.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium xenopi (bacteria) / Gene: mtr, I553_7456 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: X8E6Y0, mycothione reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Bis-tris propaan, sodium chloride, PEG 3350, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.34→63.34 Å / Num. obs: 47513 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.069 / Rrim(I) all: 0.178 / Χ2: 0.83 / Net I/σ(I): 7.3 / Num. measured all: 317955
Reflection shellResolution: 2.34→2.47 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.895 / Num. measured all: 46567 / Num. unique obs: 6850 / CC1/2: 0.673 / Rpim(I) all: 0.787 / Rrim(I) all: 2.055 / Χ2: 0.63 / Net I/σ(I) obs: 1.1

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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: 2.34→63.34 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 2284 4.85 %
Rwork0.2328 --
obs0.235 47058 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→63.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 202 65 7317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057408
X-RAY DIFFRACTIONf_angle_d0.71710108
X-RAY DIFFRACTIONf_dihedral_angle_d10.1581098
X-RAY DIFFRACTIONf_chiral_restr0.051144
X-RAY DIFFRACTIONf_plane_restr0.0071296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.390.40871400.40222566X-RAY DIFFRACTION92
2.39-2.450.38151310.36712658X-RAY DIFFRACTION96
2.45-2.510.37071620.33742766X-RAY DIFFRACTION98
2.51-2.580.3741600.32422810X-RAY DIFFRACTION99
2.58-2.650.38241550.31192747X-RAY DIFFRACTION100
2.65-2.740.35471470.29462780X-RAY DIFFRACTION100
2.74-2.830.29771170.28242840X-RAY DIFFRACTION100
2.83-2.950.31641420.28942831X-RAY DIFFRACTION100
2.95-3.080.36821220.29372818X-RAY DIFFRACTION100
3.08-3.240.37071390.28392841X-RAY DIFFRACTION100
3.24-3.450.31381470.26262831X-RAY DIFFRACTION100
3.45-3.710.28971470.24382803X-RAY DIFFRACTION100
3.71-4.090.26051510.21022823X-RAY DIFFRACTION100
4.09-4.680.19951380.17272858X-RAY DIFFRACTION100
4.68-5.890.2191400.1792877X-RAY DIFFRACTION100
5.89-63.340.20171460.16672925X-RAY DIFFRACTION100

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