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- PDB-9lwz: Crystal structure of the oxidized state of thioredoxin gluthathio... -

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Basic information

Entry
Database: PDB / ID: 9lwz
TitleCrystal structure of the oxidized state of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation SjTGR-U597C-oxidized
Componentsthioredoxin-disulfide reductase
KeywordsOXIDOREDUCTASE / SjTGR
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.074 Å
AuthorsWang, S.Q. / Huang, S.Q. / Lin, T.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plos Pathog. / Year: 2026
Title: Structural basis for substrate recognition and inhibition of thioredoxin glutathione reductase from Schistosoma japonicum: Implications for antiparasitic development.
Authors: Wang, S. / Hong, W. / Zhong, S. / Liang, Z. / Xiao, T. / Zhang, C. / Liu, X. / Dai, Z. / Li, Y. / Wu, S. / Cai, Q. / Wu, C. / Huang, Y. / Hong, P. / Ren, H. / Li, S. / Lin, T. / Chen, X. / Huang, S.
History
DepositionFeb 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.1May 6, 2026Group: Structure summary / Category: entity / Item: _entity.details
Revision 1.2May 27, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thioredoxin-disulfide reductase
B: thioredoxin-disulfide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,93710
Polymers130,2282
Non-polymers1,7098
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11160 Å2
ΔGint-134 kcal/mol
Surface area45990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.810, 86.616, 182.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein thioredoxin-disulfide reductase


Mass: 65114.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The author claimed this entity(chain) contains SEC(U)597C mutation. NCBI accession number is PZ269544.1
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Gene: EWB00_006158 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: thioredoxin-disulfide reductase (NADPH)
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 4% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350

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Data collection

DiffractionMean temperature: 295.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.07→91.29 Å / Num. obs: 81335 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2.07→2.19 Å / Num. unique obs: 11742 / CC1/2: 0.454

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.074→91.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.242 / SU ML: 0.154 / Cross valid method: NONE / ESU R: 0.2 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2389 3903 4.807 %
Rwork0.1928 77286 -
all0.195 --
obs-81189 99.913 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.208 Å2
Baniso -1Baniso -2Baniso -3
1--0.336 Å2-0 Å2-0 Å2
2---0.237 Å20 Å2
3---0.572 Å2
Refinement stepCycle: LAST / Resolution: 2.074→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9048 0 112 306 9466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129359
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168834
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.81812697
X-RAY DIFFRACTIONr_angle_other_deg0.5681.75420413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30251186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.226535
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.114102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.719101597
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.53510381
X-RAY DIFFRACTIONr_chiral_restr0.0770.21443
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022001
X-RAY DIFFRACTIONr_nbd_refined0.2240.21847
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.27965
X-RAY DIFFRACTIONr_nbtor_refined0.1790.24678
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2373
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2390.21
X-RAY DIFFRACTIONr_metal_ion_refined0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.220
X-RAY DIFFRACTIONr_nbd_other0.2440.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2110.22
X-RAY DIFFRACTIONr_mcbond_it3.8054.264744
X-RAY DIFFRACTIONr_mcbond_other3.8034.264743
X-RAY DIFFRACTIONr_mcangle_it5.1297.6425930
X-RAY DIFFRACTIONr_mcangle_other5.1287.6425931
X-RAY DIFFRACTIONr_scbond_it4.5264.6454615
X-RAY DIFFRACTIONr_scbond_other4.5264.6454616
X-RAY DIFFRACTIONr_scangle_it6.5688.3516767
X-RAY DIFFRACTIONr_scangle_other6.5688.356768
X-RAY DIFFRACTIONr_lrange_it8.13142.21310564
X-RAY DIFFRACTIONr_lrange_other8.13242.2310547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.074-2.1280.3432570.32556100.32659200.890.90199.10470.326
2.128-2.1860.3163130.29654850.29758070.9270.93199.8450.295
2.186-2.2490.2772630.27453510.27456160.9440.94699.96440.27
2.249-2.3190.2922520.24952300.25154840.9410.95899.96350.237
2.319-2.3950.282770.2450210.24252980.9470.9631000.221
2.395-2.4790.2752360.23549280.23751650.950.96599.98060.211
2.479-2.5720.2982580.22446750.22849330.9460.971000.197
2.572-2.6770.2422000.20845940.2147940.9690.9751000.18
2.677-2.7960.2651890.20644300.20946190.9550.9741000.177
2.796-2.9320.292560.20641180.2143740.9480.9741000.181
2.932-3.0910.262070.2140130.21242200.9580.9721000.185
3.091-3.2780.2711920.20637410.20939330.9560.9741000.189
3.278-3.5040.2572080.21335510.21537590.9580.9761000.201
3.504-3.7840.2411680.19833410.235090.9670.981000.192
3.784-4.1450.1981570.16730750.16932320.9780.9861000.169
4.145-4.6330.1621430.12827910.12929340.9870.9911000.138
4.633-5.3470.2011130.13624960.13926090.9810.9911000.15
5.347-6.5430.2161000.1621370.16322370.9770.9891000.17
6.543-9.230.144750.12816920.12917670.990.9911000.147
9.23-91.290.215390.16510070.16710470.9710.9899.90450.223

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