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- PDB-9xub: Crystal Structure of Thioredoxin reductase from Mycobacterium tub... -

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Basic information

Entry
Database: PDB / ID: 9xub
TitleCrystal Structure of Thioredoxin reductase from Mycobacterium tuberculosis.
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase / Mycobacterium tuberculosis
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 / Thioredoxin reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, Z.Y. / Niu, W.C. / Gong, Y. / Xu, Y.C. / Cao, P.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentKZ202210005001 China
CitationJournal: Int J Mol Sci / Year: 2026
Title: Structural and Mechanistic Characterization of Mycobacterium tuberculosis TrxR Inhibition by Glutathione-Coated Gold Nanocluster.
Authors: Li, Z. / Niu, W. / Xia, D. / Chen, Y. / Chen, S. / Zhang, B. / Wang, J. / Zhu, H. / Yang, H. / Xie, F. / Zhou, Y. / Gong, Y. / Xu, Y. / Cao, P.
History
DepositionNov 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2026Group: Database references / Category: citation
Item: _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
C: Thioredoxin reductase
D: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,7548
Polymers131,6124
Non-polymers3,1424
Water8,233457
1
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3774
Polymers65,8062
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-7 kcal/mol
Surface area23070 Å2
MethodPISA
2
C: Thioredoxin reductase
D: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3774
Polymers65,8062
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-9 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.354, 107.600, 220.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Thioredoxin reductase / TR / TRXR


Mass: 32902.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: trxB, trxB2, MT4032 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WHH0, thioredoxin-disulfide reductase (NADPH)
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M Ammonium nitrate PH 6.2,20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36652 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 31.37 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.032 / Net I/σ(I): 21.3
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 0.425 / Num. unique obs: 3630 / Rpim(I) all: 0.115

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.41 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4792
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 1904 5.19 %
Rwork0.1796 34748 -
obs0.1824 36652 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.08 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 212 472 9132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738813
X-RAY DIFFRACTIONf_angle_d0.920412006
X-RAY DIFFRACTIONf_chiral_restr0.0531383
X-RAY DIFFRACTIONf_plane_restr0.00621557
X-RAY DIFFRACTIONf_dihedral_angle_d24.83263081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.26561290.18782430X-RAY DIFFRACTION99.88
2.67-2.740.2521360.17262455X-RAY DIFFRACTION99.96
2.74-2.820.27621330.1762491X-RAY DIFFRACTION99.92
2.82-2.910.29031220.18992466X-RAY DIFFRACTION99.96
2.91-3.010.27091440.19812436X-RAY DIFFRACTION100
3.01-3.130.24731240.20162454X-RAY DIFFRACTION99.81
3.13-3.280.26071310.18942474X-RAY DIFFRACTION100
3.28-3.450.27571270.18932482X-RAY DIFFRACTION99.92
3.45-3.660.22871320.17572501X-RAY DIFFRACTION99.96
3.66-3.950.21911640.16812438X-RAY DIFFRACTION100
3.95-4.340.19941320.15042494X-RAY DIFFRACTION100
4.34-4.970.17161450.14682506X-RAY DIFFRACTION100
4.97-6.260.2551390.19362521X-RAY DIFFRACTION99.96
6.26-43.410.2111460.20732600X-RAY DIFFRACTION98.71

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