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- PDB-9g92: Crystal structure of thioredoxin reductase from Cryptosporidium p... -

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Basic information

Entry
Database: PDB / ID: 9g92
TitleCrystal structure of thioredoxin reductase from Cryptosporidium parvum in the "in" conformation
ComponentsThioredoxin reductase
KeywordsFLAVOPROTEIN / reductase
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / 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
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 / DI(HYDROXYETHYL)ETHER / Thioredoxin reductase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGabriele, F. / Palerma, M. / Ardini, M. / Bogard, J. / Chen, X.M. / Williams, D.L. / Angelucci, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI177493 United States
CitationJournal: 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
DepositionJul 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 28, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Thioredoxin reductase
BBB: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5408
Polymers112,6012
Non-polymers1,9406
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-60 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.866, 74.323, 188.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 25 - 520 / Label seq-ID: 25 - 520

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Thioredoxin reductase


Mass: 56300.410 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
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, 5mM DTT

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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 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→39.868 Å / Num. obs: 75521 / % possible obs: 99.9 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2 / Net I/σ(I): 14.1
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 1.229 / Num. unique obs: 7480 / CC1/2: 0.831

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.868 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.567 / SU ML: 0.101 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2123 3917 5.187 %
Rwork0.1772 71593 -
all0.179 --
obs-75510 99.919 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.013 Å2
Baniso -1Baniso -2Baniso -3
1--0.769 Å20 Å2-0 Å2
2--0.061 Å20 Å2
3---0.708 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7546 0 128 477 8151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0137925
X-RAY DIFFRACTIONr_bond_other_d0.0090.0157514
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.63810754
X-RAY DIFFRACTIONr_angle_other_deg1.3611.57717385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06951026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45422.886343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.952151327
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg8.271158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0031534
X-RAY DIFFRACTIONr_chiral_restr0.0780.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029658
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021704
X-RAY DIFFRACTIONr_nbd_refined0.2010.21434
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.26877
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23897
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2475
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0320.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.234
X-RAY DIFFRACTIONr_nbd_other0.2710.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.215
X-RAY DIFFRACTIONr_mcbond_it2.0092.4854035
X-RAY DIFFRACTIONr_mcbond_other2.0052.4844033
X-RAY DIFFRACTIONr_mcangle_it2.8173.7185054
X-RAY DIFFRACTIONr_mcangle_other2.8163.7185054
X-RAY DIFFRACTIONr_scbond_it2.6652.773890
X-RAY DIFFRACTIONr_scbond_other2.6642.7713891
X-RAY DIFFRACTIONr_scangle_it4.0364.0175690
X-RAY DIFFRACTIONr_scangle_other4.0364.0185691
X-RAY DIFFRACTIONr_lrange_it5.27928.9918725
X-RAY DIFFRACTIONr_lrange_other5.24428.8898649
X-RAY DIFFRACTIONr_ncsr_local_group_10.0730.0515331
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.073420.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.073420.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.272970.2245200X-RAY DIFFRACTION100
2.001-2.0550.2592780.2055070X-RAY DIFFRACTION99.7203
2.055-2.1150.2473050.1954934X-RAY DIFFRACTION100
2.115-2.180.2442180.1854868X-RAY DIFFRACTION99.9607
2.18-2.2510.2272450.1794671X-RAY DIFFRACTION100
2.251-2.330.2382530.1764526X-RAY DIFFRACTION99.9791
2.33-2.4170.2272140.174385X-RAY DIFFRACTION100
2.417-2.5150.2372400.174188X-RAY DIFFRACTION99.7972
2.515-2.6270.1992350.1664040X-RAY DIFFRACTION99.9766
2.627-2.7540.2081820.1763909X-RAY DIFFRACTION99.9756
2.754-2.9030.1912120.1693666X-RAY DIFFRACTION99.897
2.903-3.0780.2132060.1763496X-RAY DIFFRACTION99.919
3.078-3.2890.2051790.1743278X-RAY DIFFRACTION99.9711
3.289-3.550.2241770.1763086X-RAY DIFFRACTION99.9081
3.55-3.8860.2181620.1772844X-RAY DIFFRACTION100
3.886-4.340.1911270.1572627X-RAY DIFFRACTION100
4.34-5.0010.1621360.1542295X-RAY DIFFRACTION99.9589
5.001-6.1020.2171080.1891990X-RAY DIFFRACTION100
6.102-8.530.207760.2061574X-RAY DIFFRACTION100
8-100.158670.158946X-RAY DIFFRACTION99.2165

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