PDB-9h9c: Crystal structure of thioredoxin reductase from Cryptosporidium p...

ID or keywords:

Entry

Database: PDB / ID: 9h9c

Title

Crystal structure of thioredoxin reductase from Cryptosporidium parvum in the "activated in" conformation

Components

Putative thioredoxin reductase

Keywords

FLAVOPROTEIN / reductase

Function / homology

Function and homology information

glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Gabriele, F. / Palerma, M. / Ardini, M. / Bogard, J. / Chen, X.M. / Williams, D.L. / Angelucci, F.

Funding support

United States, 1items

Citation

Journal: Biochemistry / Year: 2025
Title: Targeting Apicomplexan Parasites: Structural and Functional Characterization of Cryptosporidium Thioredoxin Reductase as a Novel Drug Target.
Authors: Gabriele, F. / Bogard, J.A. / Palerma, M. / Ardini, M. / Byrne, M.E. / Chen, X.M. / Petukhov, P.A. / Ippoliti, R. / Angelucci, F. / Williams, D.L.

History

Deposition	Oct 30, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 14, 2025	Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	May 28, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9h9c.cif.gz	702 KB	Display	PDBx/mmCIF format
PDB format	pdb9h9c.ent.gz		Display	PDB format
PDBx/mmJSON format	9h9c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/9h9c ftp://data.pdbj.org/pub/pdb/validation_reports/h9/9h9c	HTTPS FTP

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Related structure data

Related structure data	9g92C 9gezC 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	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (8) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

AAA: Putative thioredoxin reductase

BBB: Putative thioredoxin reductase

CCC: Putative thioredoxin reductase

DDD: Putative thioredoxin reductase

hetero molecules

229 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Putative thioredoxin reductase

BBB: Putative thioredoxin reductase

hetero molecules

defined by author
Evidence: gel filtration
115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

CCC: Putative thioredoxin reductase

DDD: Putative thioredoxin reductase

hetero molecules

defined by author
115 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.872, 72.543, 188.458
Angle α, β, γ (deg.)	90.000, 90.613, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLY / End label comp-ID: GLY

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	AAA	A	24 - 517	24 - 517
2	1	1	BBB	B	24 - 517	24 - 517
3	2	2	AAA	A	24 - 521	24 - 521
4	2	2	CCC	C	24 - 521	24 - 521
5	3	3	AAA	A	24 - 518	24 - 518
6	3	3	DDD	D	24 - 518	24 - 518
7	4	4	BBB	B	24 - 517	24 - 517
8	4	4	CCC	C	24 - 517	24 - 517
9	5	5	BBB	B	24 - 517	24 - 517
10	5	5	DDD	D	24 - 517	24 - 517
11	6	6	CCC	C	24 - 518	24 - 518
12	6	6	DDD	D	24 - 518	24 - 518

NCS ensembles :

ID	Details
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

#1: Protein	Putative thioredoxin reductase Mass: 56360.504 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: CPATCC_000467 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IS93
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 2.34 Å³/Da / Density % sol: 47.42 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME, 5 mM DTT

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.4→39.91 Å / Num. obs: 78143 / % possible obs: 99.53 % / Redundancy: 6.5 % / CC_1/2: 0.996 / R_merge(I) obs: 0.12 / Net I/σ(I): 12.72
Reflection shell	Resolution: 2.4→2.486 Å / R_merge(I) obs: 0.78 / Num. unique obs: 7744 / CC_1/2: 0.79

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→39.91 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c free: 0.877 / SU B: 21.06 / SU ML: 0.253 / Cross valid method: FREE R-VALUE / ESU R: 0.634 / ESU R Free: 0.288
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2568	3930	5.03 %
R_work	0.2232	74198	-
all	0.225	-	-
obs	-	78128	99.681 %

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: 40.311 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.36 Å²	-0 Å²	-0.404 Å²
2-	-	-1.098 Å²	-0 Å²
3-	-	-	0.747 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→39.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15073	0	247	284	15604

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	15707
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.015	14913
X-RAY DIFFRACTION	r_angle_refined_deg	1.533	1.638	21289
X-RAY DIFFRACTION	r_angle_other_deg	1.274	1.577	34477
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.47	5	2005
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.701	22.924	684
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.034	15	2625
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	6.872	15	10
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.173	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	2076
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	19074
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3382
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	2838
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	13005
X-RAY DIFFRACTION	r_nbtor_refined	0.162	0.2	7533
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	6908
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	468
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.061	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.282	0.2	52
X-RAY DIFFRACTION	r_nbd_other	0.331	0.2	143
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.217	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.007	3.11	7972
X-RAY DIFFRACTION	r_mcbond_other	2.006	3.11	7971
X-RAY DIFFRACTION	r_mcangle_it	3.229	4.658	9966
X-RAY DIFFRACTION	r_mcangle_other	3.229	4.658	9967
X-RAY DIFFRACTION	r_scbond_it	2.078	3.317	7735
X-RAY DIFFRACTION	r_scbond_other	2.079	3.317	7736
X-RAY DIFFRACTION	r_scangle_it	3.369	4.862	11314
X-RAY DIFFRACTION	r_scangle_other	3.369	4.862	11315
X-RAY DIFFRACTION	r_lrange_it	5.265	35.349	16689
X-RAY DIFFRACTION	r_lrange_other	5.264	35.349	16674
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.051	0.05	15090
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.043	0.05	15274
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.048	0.05	15151
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.05	0.05	15087
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.041	0.05	15152
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.048	0.05	15218

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.05142	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.05142	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.04344	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.04344	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.04773	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.04773	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.04968	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.04968	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.04104	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.04104	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.04778	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.04778	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 (%)
2.4-2.462	0.292	266	0.257	5492	X-RAY DIFFRACTION	99.9826
2.462-2.529	0.311	270	0.246	5287	X-RAY DIFFRACTION	100
2.529-2.602	0.305	265	0.253	5165	X-RAY DIFFRACTION	100
2.602-2.682	0.357	197	0.357	5047	X-RAY DIFFRACTION	98.6827
2.682-2.77	0.276	249	0.245	4864	X-RAY DIFFRACTION	99.9218
2.77-2.866	0.282	295	0.228	4678	X-RAY DIFFRACTION	100
2.866-2.974	0.306	259	0.222	4523	X-RAY DIFFRACTION	99.9791
2.974-3.095	0.274	281	0.217	4326	X-RAY DIFFRACTION	99.9133
3.095-3.231	0.259	243	0.208	4198	X-RAY DIFFRACTION	99.9325
3.231-3.388	0.253	205	0.204	4014	X-RAY DIFFRACTION	99.9053
3.388-3.57	0.293	237	0.268	3785	X-RAY DIFFRACTION	98.8935
3.57-3.785	0.262	235	0.238	3552	X-RAY DIFFRACTION	99.1881
3.785-4.043	0.243	166	0.237	3412	X-RAY DIFFRACTION	99.1136
4.043-4.364	0.204	172	0.174	3198	X-RAY DIFFRACTION	99.8814
4.364-4.774	0.205	173	0.166	2915	X-RAY DIFFRACTION	99.9029
4.774-5.328	0.208	97	0.191	2724	X-RAY DIFFRACTION	99.7878
5.328-6.135	0.208	134	0.197	2386	X-RAY DIFFRACTION	99.8415
6.135-7.47	0.248	82	0.193	2044	X-RAY DIFFRACTION	99.8122
7.47-10.384	0.198	81	0.176	1607	X-RAY DIFFRACTION	99.7636
10.384-39.9	0.273	23	0.247	981	X-RAY DIFFRACTION	99.0138

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.6909	-0.2498	-0.2954	0.1607	0.2061	0.268	0.0673	-0.0582	-0.0122	-0.0603	-0.0449	-0.0156	-0.0788	-0.0641	-0.0224	0.0776	0.0127	0.0143	0.1456	-0.0117	0.0222	15.0579	2.3599	31.8469
2	0.3894	-0.2565	-0.2395	0.4055	0.3319	0.2834	0.0353	0.0883	-0.0904	-0.0747	-0.039	-0.0085	-0.0722	-0.012	0.0037	0.0741	-0.0121	0.017	0.1383	-0.0247	0.0425	38.1928	-19.1211	15.6179
3	0.8329	0.2858	0.4177	0.1879	0.1403	0.218	-0.057	0.0419	-0.0769	0.0074	0.0922	-0.0287	-0.0317	-0.0188	-0.0352	0.0126	0.029	0.004	0.2321	-0.0175	0.008	51.6735	0.3405	63.2229
4	0.9321	0.1153	0.1567	0.5546	0.2005	0.1046	-0.0988	-0.2639	0.1263	-0.0133	0.0877	-0.0675	-0.041	-0.0526	0.0111	0.0432	0.0933	-0.0351	0.2315	-0.0976	0.0444	74.5803	22.7503	78.3284

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	24 - 521
2	X-RAY DIFFRACTION	2	ALL	BBB	24 - 518
3	X-RAY DIFFRACTION	3	ALL	CCC	24 - 521
4	X-RAY DIFFRACTION	4	ALL	DDD	24 - 519

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