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- PDB-22fd: Crystal structure of thioredoxin gluthathione reductase from Schi... -

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Basic information

Entry
Database: PDB / ID: 22fd
TitleCrystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum with the U597C mutation in complex with NADPH
Componentsthioredoxin-disulfide reductase (NADPH)
KeywordsOXIDOREDUCTASE / TGR
Function / homology2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / MALONIC ACID
Function and homology information
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJan 8, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 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

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Assembly

Deposited unit
A: thioredoxin-disulfide reductase (NADPH)
B: thioredoxin-disulfide reductase (NADPH)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,0228
Polymers130,2282
Non-polymers2,7946
Water9,710539
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12800 Å2
ΔGint-109 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.220, 86.360, 183.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: CYS / End label comp-ID: CYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 7 - 596 / Label seq-ID: 7 - 596

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein thioredoxin-disulfide reductase (NADPH)


Mass: 65114.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 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-ATR / 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
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: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.9→61.2 Å / Num. obs: 106193 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 1.9→1.95 Å / Num. unique obs: 7791 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→60.368 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.642 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2273 5351 5.043 %
Rwork0.1898 100752 -
all0.192 --
obs-106103 99.978 %
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: 32.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.729 Å20 Å2-0 Å2
2---1.15 Å20 Å2
3---1.879 Å2
Refinement stepCycle: LAST / Resolution: 1.9→60.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9050 0 182 539 9771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129492
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168915
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.82312895
X-RAY DIFFRACTIONr_angle_other_deg0.5351.75620606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78951196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.232537
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg12.57416.6676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.386101612
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.8610384
X-RAY DIFFRACTIONr_chiral_restr0.0770.21464
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210979
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022029
X-RAY DIFFRACTIONr_nbd_refined0.2170.21789
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.28036
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24744
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2559
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2470.220
X-RAY DIFFRACTIONr_nbd_other0.2460.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.210
X-RAY DIFFRACTIONr_mcbond_it2.7393.2514769
X-RAY DIFFRACTIONr_mcbond_other2.7393.254768
X-RAY DIFFRACTIONr_mcangle_it3.6065.8245970
X-RAY DIFFRACTIONr_mcangle_other3.6055.8245971
X-RAY DIFFRACTIONr_scbond_it3.7383.654723
X-RAY DIFFRACTIONr_scbond_other3.7373.654722
X-RAY DIFFRACTIONr_scangle_it5.5186.5566925
X-RAY DIFFRACTIONr_scangle_other5.5186.5566926
X-RAY DIFFRACTIONr_lrange_it6.7133.10810807
X-RAY DIFFRACTIONr_lrange_other6.71433.13310722
X-RAY DIFFRACTIONr_ncsr_local_group_10.0690.0518911
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.069090.05009
12AX-RAY DIFFRACTIONLocal ncs0.069090.05009
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
1.9-1.9490.3244070.27373770.27677850.9250.94499.98720.239
1.949-2.0030.2993520.24672110.24975630.9390.9571000.208
2.003-2.0610.2594190.23469610.23673810.9590.96299.98650.198
2.061-2.1240.2363570.21267450.21371020.9650.9711000.179
2.124-2.1940.2593850.2165640.21269490.9580.9721000.178
2.194-2.270.2423260.20364060.20567320.9630.9741000.171
2.27-2.3560.2963060.19661450.20164510.9530.9761000.165
2.356-2.4520.2583290.19559070.19862360.9630.9771000.165
2.452-2.5610.2463220.18857070.19160290.9650.9791000.16
2.561-2.6860.2592850.19154500.19457350.9590.9781000.167
2.686-2.8310.2432720.19952020.20154740.9620.9751000.177
2.831-3.0020.252580.20249550.20452130.9590.9751000.186
3.002-3.2090.2332480.19346230.19548720.9680.97799.97950.184
3.209-3.4650.2412310.19843300.245610.9680.9771000.193
3.465-3.7940.2231990.18740140.18942130.9730.9811000.189
3.794-4.240.1931840.16736480.16838320.9790.9851000.175
4.24-4.8920.1611640.14132490.14234130.9860.9891000.155
4.892-5.9820.2061420.18127660.18229080.9770.9861000.194
5.982-8.4180.1581090.16222010.16223100.9820.9871000.178
8.418-60.3680.153560.18512910.18413620.9890.98498.89870.205

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