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- PDB-9qs8: Crystal Structure of Mycobacterium smegmatis thioredoxin reductas... -

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Basic information

Entry
Database: PDB / ID: 9qs8
TitleCrystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z2997505083
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / TrxR / Fragment
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / MALONATE ION / Thioredoxin reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsBecker, F. / Benz, L.S. / Janssen, P. / Fuesser, F.T. / Weiss, M.S. / Kuemmel, D. / Koch, O.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO 4689/5-1 Germany
German Research Foundation (DFG)GRK 2515 Germany
German Research Foundation (DFG)FE2166/1-1 Germany
German Federal Ministry for Education and ResearchDZIF Flex Fund TTU 02.906 Germany
CitationJournal: ChemRxiv / Year: 2025
Title: Accessing Ultralarge Chemical Spaces via a Sociable Fragment Library: Design and Crystallographic Screening
Authors: Jannsen, P. / Becker, F. / Benz, L.S. / Fuesser, F.T. / Tolmachova, N. / Matviiuk, T. / Kondratov, I. / Weiss, M.S. / Kuemmel, D. / Koch, O.
History
DepositionApr 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9878
Polymers34,5791
Non-polymers1,4087
Water3,351186
1
B: Thioredoxin reductase
hetero molecules

B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,97416
Polymers69,1572
Non-polymers2,81714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)68.220, 68.220, 154.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Thioredoxin reductase


Mass: 34578.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: trxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FW12

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Non-polymers , 7 types, 193 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-A1JAC / 2-methyl-~{N}-(1-methyl-1,2,3,4-tetrazol-5-yl)-1,3-thiazole-5-carboxamide


Mass: 224.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N6OS / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2.16 M Sodium malonate dibasic monohydrate, 10% glycerol, soaked with 5% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.86→46.93 Å / Num. obs: 35825 / % possible obs: 99.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1606 / Rrim(I) all: 0.1746 / Net I/σ(I): 10.91
Reflection shellResolution: 1.86→1.926 Å / Num. unique obs: 3516 / CC1/2: 0.358

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Processing

Software
NameVersionClassification
MxCuBE2.2data collection
XDS3.1.9ddata reduction
XDS3.1.9ddata scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→46.93 Å / SU ML: 0.2906 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2414 1772 4.95 %
Rwork0.2014 34045 -
obs0.2034 35817 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 93 186 2585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852480
X-RAY DIFFRACTIONf_angle_d0.97563371
X-RAY DIFFRACTIONf_chiral_restr0.0593379
X-RAY DIFFRACTIONf_plane_restr0.0094440
X-RAY DIFFRACTIONf_dihedral_angle_d12.9627360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.910.39351300.37712570X-RAY DIFFRACTION99.89
1.91-1.970.36611330.33812593X-RAY DIFFRACTION99.96
1.97-2.030.34371370.30572573X-RAY DIFFRACTION100
2.03-2.10.30681470.2792562X-RAY DIFFRACTION99.96
2.1-2.190.28991510.25242567X-RAY DIFFRACTION99.96
2.19-2.290.26361670.23442565X-RAY DIFFRACTION99.89
2.29-2.410.2311200.20742602X-RAY DIFFRACTION100
2.41-2.560.21331200.21622615X-RAY DIFFRACTION100
2.56-2.750.26261340.19962604X-RAY DIFFRACTION100
2.75-3.030.25281180.22654X-RAY DIFFRACTION100
3.03-3.470.2231360.17662647X-RAY DIFFRACTION99.96
3.47-4.370.19571290.14852684X-RAY DIFFRACTION100
4.37-46.930.20631500.17022809X-RAY DIFFRACTION99.66

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