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- PDB-9ro3: Crystal structure of Cryptosporidium parvum Thioredoxin Reductase... -

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Basic information

Entry
Database: PDB / ID: 9ro3
TitleCrystal structure of Cryptosporidium parvum Thioredoxin Reductase in complex with the auranofin analogue AuP(OCH3)3Cl
ComponentsThioredoxin reductase
KeywordsFLAVOPROTEIN / reductase
Function / homology
Function and homology information


glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / glutathione metabolic process / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGabriele, F. / Palerma, M. / Ardini, M. / Bogard, J. / Williams, D.L. / Ippoliti, R. / Angelucci, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Gold-containing compounds target an apicomplexan Thioredoxin reductase: Disclosing reactivity through structural and functional characterization.
Authors: Gabriele, F. / Palerma, M. / Bogard, J. / Paluzzi, L. / Zineddu, S. / Geri, A. / Vitali, V. / Massai, L. / Ardini, M. / Bellelli, A. / Petukhov, P.A. / Ippoliti, R. / Messori, L. / Williams, D.L. / Angelucci, F.
History
DepositionJun 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
C: Thioredoxin reductase
D: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,93511
Polymers225,2024
Non-polymers3,7337
Water4,684260
1
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5666
Polymers112,6012
Non-polymers1,9654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint-78 kcal/mol
Surface area37670 Å2
MethodPISA
2
C: Thioredoxin reductase
D: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3695
Polymers112,6012
Non-polymers1,7683
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-65 kcal/mol
Surface area37640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.296, 73.251, 189.519
Angle α, β, γ (deg.)90.00, 90.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Thioredoxin reductase


Mass: 56300.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: TRx / Production host: Escherichia coli (E. coli) / References: UniProt: C8CCG0
#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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME / PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.56 Å / Num. obs: 102375 / % possible obs: 98.67 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 8.84
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 10135 / CC1/2: 0.537

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.645 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 5056 4.9 %RANDOM
Rwork0.20418 ---
obs0.206 97310 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-1.29 Å2
2--0.33 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.2→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14886 0 215 260 15361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01315539
X-RAY DIFFRACTIONr_bond_other_d0.0080.01514729
X-RAY DIFFRACTIONr_angle_refined_deg1.521.63821088
X-RAY DIFFRACTIONr_angle_other_deg1.2831.57634072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16951995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51822.903682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.792152611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3751567
X-RAY DIFFRACTIONr_chiral_restr0.0710.22073
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023348
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2664.4977878
X-RAY DIFFRACTIONr_mcbond_other4.2634.4967877
X-RAY DIFFRACTIONr_mcangle_it5.7386.7319853
X-RAY DIFFRACTIONr_mcangle_other5.7386.7329854
X-RAY DIFFRACTIONr_scbond_it4.9284.9517661
X-RAY DIFFRACTIONr_scbond_other4.9284.9527658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1437.2111218
X-RAY DIFFRACTIONr_long_range_B_refined8.70351.34816319
X-RAY DIFFRACTIONr_long_range_B_other8.70851.35216292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A149450.06
12B149450.06
21A150240.04
22C150240.04
31A149340.06
32D149340.06
41B148740.06
42C148740.06
51B149650.04
52D149650.04
61C149480.06
62D149480.06
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 427 -
Rwork0.309 7078 -
obs--98.12 %

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