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- PDB-4j57: Structure of Plasmodium falciparum thioredoxin reductase-thioredo... -

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Basic information

Entry
Database: PDB / ID: 4j57
TitleStructure of Plasmodium falciparum thioredoxin reductase-thioredoxin complex
Components
  • Thioredoxin
  • Thioredoxin reductase 2
KeywordsOXIDOREDUCTASE / Protein-Protein Complex / Thioredoxin fold / Disulfide reductase / FAD binding / NADPH binding / Thioredoxin binding
Function / homology
Function and homology information


Metabolism of ingested MeSeO2H into MeSeH / The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding ...Metabolism of ingested MeSeO2H into MeSeH / The NLRP3 inflammasome / TP53 Regulates Metabolic Genes / Detoxification of Reactive Oxygen Species / Interconversion of nucleotide di- and triphosphates / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / Thioredoxin / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 ...Thioredoxin/glutathione reductase selenoprotein / Pyridine nucleotide-disulphide oxidoreductase / FAD binding domain / : / Thioredoxin / FAD/NAD-linked reductase, C-terminal dimerisation domain / 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 / Thioredoxin / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin, conserved site / Thioredoxin family active site. / Enolase-like; domain 1 / Thioredoxin domain profile. / FAD/NAD(P)-binding domain / Thioredoxin domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase / Thioredoxin 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFritz-Wolf, K. / Jortzik, E. / Stumpf, M. / Preuss, J. / Iozef, R. / Rahlfs, S. / Becker, K.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal Structure of the Plasmodium falciparum Thioredoxin Reductase-Thioredoxin Complex.
Authors: Fritz-Wolf, K. / Jortzik, E. / Stumpf, M. / Preuss, J. / Iozef, R. / Rahlfs, S. / Becker, K.
History
DepositionFeb 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / refine / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase 2
B: Thioredoxin reductase 2
E: Thioredoxin
F: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,8767
Polymers145,2134
Non-polymers1,6633
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12740 Å2
ΔGint-87 kcal/mol
Surface area45950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.800, 100.600, 142.830
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-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 38:249 or resseq 260:534)
211chain 'B' and (resseq 38:249 or resseq 260:534)
112chain 'E'
212chain 'F'

NCS ensembles :
ID
1
2

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Components

#1: Protein Thioredoxin reductase 2 / TrxR2


Mass: 59752.160 Da / Num. of mol.: 2 / Mutation: C540S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: trxr2, PFI1170c / Plasmid: pRSETa / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P61076, thioredoxin-disulfide reductase
#2: Protein Thioredoxin / Trx


Mass: 12854.468 Da / Num. of mol.: 2 / Mutation: C33S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF14_0545 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q7KQL8
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 45.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% PEG 3000, 50 mM BisTris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9765 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 46468 / Num. obs: 46341 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 56.8 Å2 / Rsym value: 0.229 / Net I/σ(I): 7.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.9 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.997 Å / SU ML: 0.39 / σ(F): 1.99 / Phase error: 28.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 2777 6 %
Rwork0.2164 --
obs0.2194 46319 99.93 %
all-46468 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3592 Å2-0 Å20 Å2
2---6.2809 Å20 Å2
3---9.6401 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9072 0 112 25 9209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099367
X-RAY DIFFRACTIONf_angle_d1.19412659
X-RAY DIFFRACTIONf_dihedral_angle_d15.53426
X-RAY DIFFRACTIONf_chiral_restr0.0821426
X-RAY DIFFRACTIONf_plane_restr0.0051582
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3639X-RAY DIFFRACTIONPOSITIONAL
12B3639X-RAY DIFFRACTIONPOSITIONAL0.048
21E813X-RAY DIFFRACTIONPOSITIONAL
22F813X-RAY DIFFRACTIONPOSITIONAL0.021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.3511360.31092136X-RAY DIFFRACTION100
2.5431-2.58920.40261370.33192148X-RAY DIFFRACTION100
2.5892-2.63890.36721370.32422151X-RAY DIFFRACTION100
2.6389-2.69270.35681370.30992143X-RAY DIFFRACTION100
2.6927-2.75110.35291360.2872137X-RAY DIFFRACTION100
2.7511-2.81490.32491380.28412163X-RAY DIFFRACTION100
2.8149-2.88510.30911390.26842168X-RAY DIFFRACTION100
2.8851-2.96280.36841380.27442167X-RAY DIFFRACTION100
2.9628-3.04970.33641370.26212155X-RAY DIFFRACTION100
3.0497-3.14780.30471380.2532153X-RAY DIFFRACTION100
3.1478-3.25990.34861380.24982165X-RAY DIFFRACTION100
3.2599-3.38980.3011380.23042162X-RAY DIFFRACTION100
3.3898-3.54320.29791380.22312164X-RAY DIFFRACTION100
3.5432-3.72890.25431400.21642188X-RAY DIFFRACTION100
3.7289-3.96090.26521390.20242178X-RAY DIFFRACTION100
3.9609-4.26390.21891400.17922190X-RAY DIFFRACTION100
4.2639-4.6880.17641400.16342193X-RAY DIFFRACTION100
4.688-5.3550.24061410.17132230X-RAY DIFFRACTION100
5.355-6.70420.22351430.19692239X-RAY DIFFRACTION100
6.7042-19.99770.20671470.16062312X-RAY DIFFRACTION99

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