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

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Basic information

Entry
Database: PDB / ID: 9qse
TitleCrystal Structure of Mycobacterium smegmatis thioredoxin reductase in complex with Z30008604
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: 1.97 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
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9267
Polymers34,5791
Non-polymers1,3476
Water2,954164
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,85214
Polymers69,1572
Non-polymers2,69512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4_555y,x,-z1
MethodPISA
Unit cell
Length a, b, c (Å)67.690, 67.690, 155.360
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
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 , 6 types, 170 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-A1I96 / ~{N}-(4,5-dihydro-1,3-thiazol-2-yl)-2,4-dimethyl-1,3-thiazole-5-carboxamide


Mass: 241.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N3OS2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
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 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: 1.97→46.79 Å / Num. obs: 29988 / % possible obs: 99.92 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.92 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.14
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 2952 / CC1/2: 0.39

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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: 1.97→46.79 Å / SU ML: 0.2721 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9694
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2412 1498 5 %
Rwork0.2032 28487 -
obs0.2051 29985 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.61 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 89 164 2559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092468
X-RAY DIFFRACTIONf_angle_d1.05853355
X-RAY DIFFRACTIONf_chiral_restr0.0557378
X-RAY DIFFRACTIONf_plane_restr0.009437
X-RAY DIFFRACTIONf_dihedral_angle_d13.0922362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.35491460.34352516X-RAY DIFFRACTION99.96
2.03-2.110.34051380.31332560X-RAY DIFFRACTION100
2.11-2.190.34851600.28122521X-RAY DIFFRACTION99.96
2.19-2.290.31211700.26242507X-RAY DIFFRACTION99.93
2.29-2.410.26021050.23552596X-RAY DIFFRACTION99.89
2.41-2.560.24221180.23272580X-RAY DIFFRACTION100
2.56-2.760.22041280.2132569X-RAY DIFFRACTION100
2.76-3.040.22271260.19572604X-RAY DIFFRACTION99.96
3.04-3.480.23591380.16652610X-RAY DIFFRACTION99.96
3.48-4.370.16461210.14632653X-RAY DIFFRACTION100
4.38-46.790.21971480.18022771X-RAY DIFFRACTION99.69

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