PDB-22fj: Crystal structure of the oxidized state of Trx1 from Schistosoma ...

ID or keywords:

Entry

Database: PDB / ID: 22fj

Title

Crystal structure of the oxidized state of Trx1 from Schistosoma japonicum

Components

Thioredoxin

Keywords

OXIDOREDUCTASE / Thioredoxin-1

Function / homology

Thioredoxin / Thioredoxin / Thioredoxin family active site. / protein-disulfide reductase activity / Thioredoxin, conserved site / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / Thioredoxin

Function and homology information

Biological species

Schistosoma japonicum (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.66 Å

Authors

Wang, S.Q. / Huang, S.Q. / Lin, T.W.

Funding support

China, 1items

Citation

Journal: 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

Deposition	Jan 8, 2026	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 15, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 27, 2026	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	22fj.cif.gz	119 KB	Display	PDBx/mmCIF format
PDB format	pdb22fj.ent.gz	89.4 KB	Display	PDB format
PDBx/mmJSON format	22fj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2f/22fj ftp://data.pdbj.org/pub/pdb/validation_reports/2f/22fj	HTTPS FTP

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Related structure data

Related structure data	22eyC 22fcC 22fdC 22feC 22ffC 22fgC 22fhC 22fkC 9lwmC 9lwzC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (4) #91 - Jul 2007 Thymine Dimers similarity (4)

Deposited unit

A: Thioredoxin

B: Thioredoxin

C: Thioredoxin

D: Thioredoxin

E: Thioredoxin

59.7 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Thioredoxin

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Thioredoxin

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Thioredoxin

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Thioredoxin

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Thioredoxin

defined by author
11.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.535, 90.533, 150.042
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	MET	MET	LYS	LYS	1 - 106	1 - 106
2	1	1	MET	MET	LYS	LYS	1 - 106	1 - 106
3	2	2	SER	SER	HIS	HIS	2 - 105	2 - 105
4	2	2	SER	SER	HIS	HIS	2 - 105	2 - 105
5	3	3	SER	SER	HIS	HIS	2 - 105	2 - 105
6	3	3	SER	SER	HIS	HIS	2 - 105	2 - 105
7	4	4	SER	SER	HIS	HIS	2 - 105	2 - 105
8	4	4	SER	SER	HIS	HIS	2 - 105	2 - 105
9	5	5	SER	SER	HIS	HIS	2 - 105	2 - 105
10	5	5	SER	SER	HIS	HIS	2 - 105	2 - 105
11	6	6	SER	SER	HIS	HIS	2 - 105	2 - 105
12	6	6	SER	SER	HIS	HIS	2 - 105	2 - 105
13	7	7	SER	SER	HIS	HIS	2 - 105	2 - 105
14	7	7	SER	SER	HIS	HIS	2 - 105	2 - 105
15	8	8	SER	SER	LYS	LYS	2 - 106	2 - 106
16	8	8	SER	SER	LYS	LYS	2 - 106	2 - 106
17	9	9	SER	SER	LYS	LYS	2 - 106	2 - 106
18	9	9	SER	SER	LYS	LYS	2 - 106	2 - 106
19	10	10	SER	SER	LYS	LYS	2 - 106	2 - 106
20	10	10	SER	SER	LYS	LYS	2 - 106	2 - 106

NCS ensembles :

ID	Details (eV)
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20

#1: Protein	Thioredoxin / Thioredoxin-1 Mass: 11938.670 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1L9K4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.31 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.66→50 Å / Num. obs: 15762 / % possible obs: 95.7 % / Redundancy: 3.8 % / CC_1/2: 0.97 / Net I/σ(I): 7.588
Reflection shell	Resolution: 2.66→2.71 Å / Num. unique obs: 720 / CC_1/2: 0.653

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.66→43.375 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.869 / SU B: 14.573 / SU ML: 0.298 / Cross valid method: FREE R-VALUE / ESU R Free: 0.427
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2845	771	5.104 %
R_work	0.2211	14336	-
all	0.224	-	-
obs	-	15107	91.425 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 51.385 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.114 Å²	0 Å²	0 Å²
2-	-	0.467 Å²	-0 Å²
3-	-	-	-0.353 Å²

Refinement step

Cycle: LAST / Resolution: 2.66→43.375 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4161	0	0	49	4210

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4231
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4103
X-RAY DIFFRACTION	r_angle_refined_deg	1.539	1.828	5720
X-RAY DIFFRACTION	r_angle_other_deg	0.522	1.794	9482
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.242	5	522
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.667	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.255	10	771
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.188	10	190
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	672
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4804
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	882
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	795
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	3493
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2060
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	2276
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.316	0.2	88
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.184	0.2	28
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	115
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.238	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	4.764	4.902	2103
X-RAY DIFFRACTION	r_mcbond_other	4.746	4.902	2103
X-RAY DIFFRACTION	r_mcangle_it	7.435	8.784	2620
X-RAY DIFFRACTION	r_mcangle_other	7.434	8.787	2621
X-RAY DIFFRACTION	r_scbond_it	5.181	5.41	2128
X-RAY DIFFRACTION	r_scbond_other	5.18	5.413	2129
X-RAY DIFFRACTION	r_scangle_it	8.411	9.683	3100
X-RAY DIFFRACTION	r_scangle_other	8.41	9.685	3101
X-RAY DIFFRACTION	r_lrange_it	13.017	60.031	17289
X-RAY DIFFRACTION	r_lrange_other	13.017	60.036	17288
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.07	0.05	3370
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	3261
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.098	0.05	3215
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.072	0.05	3276
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.083	0.05	3245
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.095	0.05	3219
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.086	0.05	3246
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.092	0.05	3250
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.075	0.05	3317
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.096	0.05	3241

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07029	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07029	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07351	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07351	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09848	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09848	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07218	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07218	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08259	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08259	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0945	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0945	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08552	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08552	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.09178	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.09178	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.07518	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.07518	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.09639	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.09639	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.66-2.709	0.34	42	0.254	814	X-RAY DIFFRACTION	73.9844
2.709-2.783	0.364	56	0.282	940	X-RAY DIFFRACTION	84.5501
2.783-2.864	0.393	60	0.302	926	X-RAY DIFFRACTION	86.9489
2.864-2.951	0.338	44	0.294	935	X-RAY DIFFRACTION	89.8165
2.951-3.048	0.368	48	0.27	906	X-RAY DIFFRACTION	87.1233
3.048-3.154	0.377	38	0.267	888	X-RAY DIFFRACTION	91.774
3.154-3.273	0.353	43	0.243	889	X-RAY DIFFRACTION	91.6421
3.273-3.405	0.306	31	0.219	845	X-RAY DIFFRACTION	91.7278
3.405-3.556	0.29	57	0.221	824	X-RAY DIFFRACTION	93.6238
3.556-3.728	0.297	29	0.206	798	X-RAY DIFFRACTION	93.9773
3.728-3.928	0.247	49	0.203	790	X-RAY DIFFRACTION	96.3261
3.928-4.164	0.216	40	0.194	732	X-RAY DIFFRACTION	97.598
4.164-4.449	0.136	42	0.164	701	X-RAY DIFFRACTION	95.9948
4.449-4.801	0.269	34	0.156	676	X-RAY DIFFRACTION	99.3007
4.801-5.253	0.249	41	0.188	598	X-RAY DIFFRACTION	98.0061
5.253-5.862	0.256	28	0.193	577	X-RAY DIFFRACTION	98.2143
5.862-6.749	0.289	36	0.216	506	X-RAY DIFFRACTION	98.5455
6.749-8.216	0.326	27	0.209	428	X-RAY DIFFRACTION	97.6395
8.216-11.416	0.224	15	0.204	339	X-RAY DIFFRACTION	93.6508
11.416-43.375	0.404	11	0.343	224	X-RAY DIFFRACTION	94.7581

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