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- PDB-7ytv: Crystal structure of Aspergillus fumigatus Thioredoxin reductase ... -

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Basic information

Entry
Database: PDB / ID: 7ytv
TitleCrystal structure of Aspergillus fumigatus Thioredoxin reductase in complex with auranofin
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase / reductase / auranofin
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.866 Å
AuthorsLin, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81903526 China
CitationJournal: J Mycol Med / Year: 2023
Title: In vitro antifungal and antibiofilm activities of auranofin against itraconazole-resistant Aspergillus fumigatus.
Authors: Chen, P. / Yang, J. / Jin, Y. / Lu, C. / Feng, Z. / Gao, F. / Chen, Y. / Wang, F. / Shang, Z. / Lin, W.
History
DepositionAug 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)82,7826
Polymers79,7242
Non-polymers3,0584
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-37 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.814, 152.814, 135.178
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Thioredoxin reductase


Mass: 39862.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: TRR1, CDV57_04819, CNMCM8057_004823 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A229Y1X4, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 5.72 Å3/Da / Density % sol: 78.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium phosphate monobasic monohydrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.866→132.34 Å / Num. obs: 17428 / % possible obs: 99.8 % / Redundancy: 19.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.062 / Rrim(I) all: 0.27 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.87-4.0820.11.6075054325190.7510.3661.6492.4100
12.23-132.3413.10.0975465770.9880.0280.0952895.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BPY

6bpy


Resolution: 3.866→59.432 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 840 4.83 %
Rwork0.2295 16544 -
obs0.2302 17384 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.59 Å2 / Biso mean: 143.1834 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.866→59.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 168 1 4858
Biso mean--172.65 80.84 -
Num. residues----638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.866-4.10820.31811630.2912695100
4.1082-4.42520.25921470.23962732100
4.4252-4.87040.25081150.22342757100
4.8704-5.57470.26491340.24312757100
5.5747-7.02170.31140.24872802100
7.0217-59.4320.20191670.2021280198

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