PDB-22fk: Crystal structure of the reduced state of Trx1 from Schistosoma j...

ID or keywords:

Entry

Database: PDB / ID: 22fk

Title

Crystal structure of the reduced 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: 1.898 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	22fk.cif.gz	120.7 KB	Display	PDBx/mmCIF format
PDB format	pdb22fk.ent.gz	90.7 KB	Display	PDB format
PDBx/mmJSON format	22fk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	22eyC 22fcC 22fdC 22feC 22ffC 22fgC 22fhC 22fjC 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)	39.916, 90.859, 151.372
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	MET	MET	LYS	LYS	1 - 106	1 - 106
6	3	3	MET	MET	LYS	LYS	1 - 106	1 - 106
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	MET	MET	LYS	LYS	1 - 106	1 - 106
12	6	6	MET	MET	LYS	LYS	1 - 106	1 - 106
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	HIS	HIS	2 - 105	2 - 105
16	8	8	SER	SER	HIS	HIS	2 - 105	2 - 105
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	HIS	HIS	2 - 105	2 - 105
20	10	10	SER	SER	HIS	HIS	2 - 105	2 - 105

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 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.: 120 / 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: 2.3 Å³/Da / Density % sol: 46.5 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop Details: 5mM DTT, 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: BL02U1 / Wavelength: 0.979183 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 31, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 1.89→50 Å / Num. obs: 43078 / % possible obs: 96.7 % / Redundancy: 9.6 % / CC_1/2: 0.999 / Net I/σ(I): 11.91
Reflection shell	Resolution: 1.9→2.01 Å / Num. unique obs: 6933 / CC_1/2: 0.472

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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: 1.898→45.43 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.947 / SU B: 5.501 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.183 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2538	2154	5 %
R_work	0.2211	40924	-
all	0.223	-	-
obs	-	43078	96.731 %

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: 46.849 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.855 Å²	-0 Å²	0 Å²
2-	-	0.426 Å²	-0 Å²
3-	-	-	-1.281 Å²

Refinement step

Cycle: LAST / Resolution: 1.898→45.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4169	0	0	120	4289

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4239
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4112
X-RAY DIFFRACTION	r_angle_refined_deg	1.568	1.829	5730
X-RAY DIFFRACTION	r_angle_other_deg	0.516	1.794	9503
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.795	5	523
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.657	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.621	10	774
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.957	10	190
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	673
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4811
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	883
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	716
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	3480
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2054
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	2357
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	124
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.171	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	4.017	4.413	2107
X-RAY DIFFRACTION	r_mcbond_other	4.017	4.413	2107
X-RAY DIFFRACTION	r_mcangle_it	6.025	7.898	2625
X-RAY DIFFRACTION	r_mcangle_other	6.024	7.9	2626
X-RAY DIFFRACTION	r_scbond_it	5.051	5.062	2132
X-RAY DIFFRACTION	r_scbond_other	5.05	5.064	2133
X-RAY DIFFRACTION	r_scangle_it	7.967	8.988	3105
X-RAY DIFFRACTION	r_scangle_other	7.966	8.99	3106
X-RAY DIFFRACTION	r_lrange_it	10.221	44.625	4449
X-RAY DIFFRACTION	r_lrange_other	10.216	44.534	4443
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	3308
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.088	0.05	3179
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.098	0.05	3190
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.083	0.05	3204
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.089	0.05	3176
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.095	0.05	3215
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.089	0.05	3196
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.09	0.05	3207
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.076	0.05	3276
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.094	0.05	3177

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	0.07307	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07307	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08771	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08771	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.09772	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.09772	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08306	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08306	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.08901	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.08901	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.095	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.095	0.05008
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08937	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08937	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.09038	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.09038	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.07613	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.07613	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.09373	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.09373	0.05009

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.898-1.947	0.431	155	0.4	2942	0.402	3198	0.869	0.871	96.8418	0.406
1.947-2.001	0.358	157	0.336	2988	0.337	3181	0.921	0.912	98.8683	0.327
2.001-2.058	0.349	150	0.31	2857	0.312	3057	0.907	0.929	98.3644	0.293
2.058-2.122	0.278	147	0.276	2800	0.276	2998	0.946	0.949	98.2989	0.251
2.122-2.191	0.299	142	0.266	2696	0.267	2882	0.94	0.954	98.4733	0.234
2.191-2.268	0.289	138	0.262	2614	0.263	2816	0.947	0.955	97.7273	0.225
2.268-2.353	0.262	134	0.242	2545	0.243	2732	0.958	0.963	98.06	0.203
2.353-2.449	0.273	126	0.252	2397	0.253	2602	0.955	0.963	96.9639	0.206
2.449-2.558	0.324	122	0.27	2317	0.273	2504	0.923	0.949	97.4042	0.226
2.558-2.682	0.338	117	0.235	2219	0.24	2427	0.935	0.967	96.2505	0.193
2.682-2.826	0.266	110	0.224	2092	0.226	2278	0.959	0.969	96.6637	0.186
2.826-2.997	0.291	105	0.242	1994	0.244	2177	0.948	0.966	96.4171	0.201
2.997-3.203	0.25	98	0.226	1873	0.227	2054	0.959	0.968	95.9591	0.198
3.203-3.458	0.244	93	0.214	1751	0.216	1925	0.959	0.973	95.7922	0.2
3.458-3.786	0.251	85	0.213	1616	0.215	1788	0.965	0.975	95.1342	0.204
3.786-4.229	0.243	76	0.196	1459	0.198	1615	0.97	0.978	95.0464	0.19
4.229-4.877	0.178	69	0.152	1296	0.154	1446	0.982	0.987	94.3983	0.16
4.877-5.956	0.177	57	0.175	1094	0.175	1241	0.988	0.985	92.7478	0.178
5.956-8.351	0.22	46	0.189	870	0.19	997	0.981	0.983	91.8756	0.194
8.351-45.43	0.176	27	0.148	504	0.149	613	0.977	0.986	86.6232	0.176

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