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- PDB-22fh: Crystal structure of the reduced state of TRP14 from Schistosoma ... -

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Basic information

Entry
Database: PDB / ID: 22fh
TitleCrystal structure of the reduced state of TRP14 from Schistosoma japonicum
ComponentsThioredoxin domain-containing protein 17
KeywordsOXIDOREDUCTASE / Thioredoxin domain-containing protein 17
Function / homologyThioredoxin domain-containing protein 17-like domain / Thioredoxin domain-containing protein 17-like / Thioredoxin domain-containing protein 17-like, thioredoxin domain / protein-disulfide reductase [NAD(P)H] activity / Thioredoxin-like superfamily / cytosol / Thioredoxin domain-containing protein 17
Function and homology information
Biological speciesSchistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.771 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 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 domain-containing protein 17
B: Thioredoxin domain-containing protein 17


Theoretical massNumber of molelcules
Total (without water)27,9322
Polymers27,9322
Non-polymers00
Water1,02757
1
A: Thioredoxin domain-containing protein 17

A: Thioredoxin domain-containing protein 17


Theoretical massNumber of molelcules
Total (without water)27,9322
Polymers27,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1440 Å2
ΔGint-6 kcal/mol
Surface area12430 Å2
MethodPISA
2
B: Thioredoxin domain-containing protein 17

B: Thioredoxin domain-containing protein 17


Theoretical massNumber of molelcules
Total (without water)27,9322
Polymers27,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.435, 38.616, 56.153
Angle α, β, γ (deg.)90.000, 90.044, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 122 / Label seq-ID: 2 - 122

Dom-ID
1
2

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

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Components

#1: Protein Thioredoxin domain-containing protein 17


Mass: 13966.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Gene: EWB00_003080 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5DDH1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 5mM DTT, 0.2 M lithium sulfate monohydrate, 0.1 M HEPES (pH 5.5), and 25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 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: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.77→38.724 Å / Num. obs: 22103 / % possible obs: 98.3 % / Redundancy: 6.2 % / CC1/2: 0.995 / Net I/σ(I): 7.9
Reflection shellResolution: 1.77→1.82 Å / Num. unique obs: 1553 / CC1/2: 0.482

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.771→38.724 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.888 / SU ML: 0.139 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2763 1081 4.891 %
Rwork0.2116 21021 -
all0.215 --
obs-22102 97.736 %
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: 35.604 Å2
Baniso -1Baniso -2Baniso -3
1-1.952 Å2-0 Å2-0.109 Å2
2---2.424 Å2-0 Å2
3---0.472 Å2
Refinement stepCycle: LAST / Resolution: 1.771→38.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 0 57 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161922
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.8562678
X-RAY DIFFRACTIONr_angle_other_deg0.5461.7824460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.879514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86210368
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.0171088
X-RAY DIFFRACTIONr_chiral_restr0.080.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_nbd_refined0.2190.2320
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21564
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2966
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.245
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0870.215
X-RAY DIFFRACTIONr_nbd_other0.1950.299
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0550.29
X-RAY DIFFRACTIONr_mcbond_it2.9033.326966
X-RAY DIFFRACTIONr_mcbond_other2.8913.324966
X-RAY DIFFRACTIONr_mcangle_it4.2035.961204
X-RAY DIFFRACTIONr_mcangle_other4.2175.9651205
X-RAY DIFFRACTIONr_scbond_it4.0893.8751014
X-RAY DIFFRACTIONr_scbond_other4.0823.8711013
X-RAY DIFFRACTIONr_scangle_it6.3216.8831474
X-RAY DIFFRACTIONr_scangle_other6.3196.8861475
X-RAY DIFFRACTIONr_lrange_it7.78441.647820
X-RAY DIFFRACTIONr_lrange_other7.78641.6517801
X-RAY DIFFRACTIONr_ncsr_local_group_10.0370.053866
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.036920.05011
12AX-RAY DIFFRACTIONLocal ncs0.036920.05011
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
1.771-1.8170.4800.36414400.36616420.8480.89492.570.364
1.817-1.8670.315690.32114740.32116010.9220.92296.37730.32
1.867-1.9210.352570.29415090.29616090.9020.92197.32750.285
1.921-1.980.372950.32813760.33115100.8110.88597.41720.317
1.98-2.0440.283970.26713690.26814950.9290.94298.06020.251
2.044-2.1160.341680.26513140.26914070.9150.94998.22320.247
2.116-2.1950.299570.22212980.22513810.9440.96998.11730.208
2.195-2.2850.262490.23212770.23313530.9520.93898.00440.208
2.285-2.3860.276670.22111730.22412610.9550.9798.33470.203
2.386-2.5020.343570.20411330.2112110.9490.97598.26590.193
2.502-2.6370.35690.2310860.23711710.9380.9798.63360.224
2.637-2.7960.376260.21210590.21611020.9510.97298.45740.211
2.796-2.9880.26590.2099930.21210710.9610.97498.2260.221
2.988-3.2260.345570.2088880.2159550.9240.97298.95290.231
3.226-3.5310.261340.188570.1838970.9660.97999.33110.208
3.531-3.9440.237330.1697700.1728120.9710.98398.89160.201
3.944-4.5460.191470.1656800.1677310.9810.98599.45280.202
4.546-5.5480.174250.1565840.1576170.9750.98798.70340.21
5.548-7.7670.238230.1994610.2014920.9470.97198.3740.272
7.767-38.7240.372120.2542800.2582940.9660.96999.31970.416

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