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

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Basic information

Entry
Database: PDB / ID: 9gez
TitleCrystal structure of thioredoxin reductase from Cryptosporidium parvum in the "waiting" position
ComponentsThioredoxin reductase
KeywordsFLAVOPROTEIN / 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
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: 2.88 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
DepositionAug 8, 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
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1724
Polymers112,6012
Non-polymers1,5712
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-73 kcal/mol
Surface area37290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.553, 74.177, 188.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 47 %
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: Sep 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.88→39.79 Å / Num. obs: 23509 / % possible obs: 96.27 % / Redundancy: 12.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.5 / Net I/σ(I): 7.56
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.83 / Num. unique obs: 2295 / CC1/2: 0.645

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→39.79 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.856 / SU B: 22.742 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26393 1199 5.2 %RANDOM
Rwork0.23127 ---
obs0.23297 22061 96.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.641 Å2
Baniso -1Baniso -2Baniso -3
1--16.69 Å20 Å20 Å2
2---6.47 Å20 Å2
3---23.16 Å2
Refinement stepCycle: 1 / Resolution: 2.88→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7508 0 106 14 7628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137818
X-RAY DIFFRACTIONr_bond_other_d0.0070.0157407
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.63810608
X-RAY DIFFRACTIONr_angle_other_deg1.21.57717138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.62751007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23423.009339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.095151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3451532
X-RAY DIFFRACTIONr_chiral_restr0.0680.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029525
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021681
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14211 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.88→2.953 Å
RfactorNum. reflection% reflection
Rfree0.258 64 -
Rwork0.212 1123 -
obs--66.39 %
Refinement TLS params.

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

IDL11 (°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)
10.30440.13320.31391.86280.27280.37640.020.0613-0.07120.1830.0753-0.3239-0.0267-0.0003-0.09530.14690.0381-0.02440.174-0.01510.06471.2983.38131.365
20.5520.61790.41341.54170.24920.397-0.04920.0368-0.0355-0.22540.11440.1193-0.0397-0.0808-0.06520.09530.0833-0.02890.27480.02490.035-21.239-20.08815.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 519
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION2B26 - 521
4X-RAY DIFFRACTION2B601

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