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

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Basic information

Entry
Database: PDB / ID: 9rte
TitleCrystal structure of Cryptosporidium parvum Thioredoxin Reductase in complex with the dicarbene Au(I) complex Au(NHC)2PF6
ComponentsPutative thioredoxin 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
DepositionJul 2, 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: Putative thioredoxin reductase
B: Putative thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,4895
Polymers112,7212
Non-polymers1,7683
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-72 kcal/mol
Surface area37500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.970, 74.291, 191.091
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 26 - 510 / Label seq-ID: 26 - 510

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Putative thioredoxin reductase


Mass: 56360.504 Da / Num. of mol.: 2
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.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME

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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: May 26, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29.4 Å / Num. obs: 53645 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Rrim(I) all: 0.13 / Χ2: 1.03 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.909 / Num. measured all: 56407 / Num. unique obs: 4590 / CC1/2: 0.955 / Rpim(I) all: 0.27 / Rrim(I) all: 0.949 / Χ2: 1.17 / Net I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.39 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.172 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25177 2643 4.9 %RANDOM
Rwork0.20753 ---
obs0.2097 50928 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.774 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å20 Å2
2--2.56 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.2→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7431 0 107 201 7739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137714
X-RAY DIFFRACTIONr_bond_other_d0.0080.0157317
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.63810461
X-RAY DIFFRACTIONr_angle_other_deg1.2841.57616913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5915978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13323340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.869151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5161532
X-RAY DIFFRACTIONr_chiral_restr0.0780.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028675
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021663
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_it3.4613.8253900
X-RAY DIFFRACTIONr_mcbond_other3.4613.8243899
X-RAY DIFFRACTIONr_mcangle_it4.7945.7284873
X-RAY DIFFRACTIONr_mcangle_other4.7935.7294874
X-RAY DIFFRACTIONr_scbond_it3.9774.1953814
X-RAY DIFFRACTIONr_scbond_other3.9774.1963811
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6956.125586
X-RAY DIFFRACTIONr_long_range_B_refined7.05443.7168253
X-RAY DIFFRACTIONr_long_range_B_other7.05343.7148222
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14866 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 215 -
Rwork0.286 3690 -
obs--99.97 %

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