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- PDB-4j56: Structure of Plasmodium falciparum thioredoxin reductase-thioredo... -

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Basic information

Entry
Database: PDB / ID: 4j56
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 (NADPH) / 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 (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / cell redox homeostasis / flavin adenine dinucleotide binding / mitochondrion / cytoplasm / cytosol
Similarity search - Function
Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin/glutathione reductase selenoprotein / 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 ...Pyridine nucleotide-disulphide oxidoreductase / Thioredoxin/glutathione reductase selenoprotein / 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: 2.371 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 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase 2
B: Thioredoxin reductase 2
C: Thioredoxin reductase 2
D: Thioredoxin reductase 2
E: Thioredoxin
F: Thioredoxin
G: Thioredoxin
H: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,56912
Polymers290,4278
Non-polymers3,1424
Water3,873215
1
A: Thioredoxin reductase 2
B: Thioredoxin reductase 2
E: Thioredoxin
F: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7846
Polymers145,2134
Non-polymers1,5712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13600 Å2
ΔGint-94 kcal/mol
Surface area46840 Å2
MethodPISA
2
C: Thioredoxin reductase 2
D: Thioredoxin reductase 2
G: Thioredoxin
H: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7846
Polymers145,2134
Non-polymers1,5712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-94 kcal/mol
Surface area46940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.880, 89.180, 151.330
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

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)
311chain 'C' and (resseq 38:249 or resseq 260:534)
411chain 'D' and (resseq 38:249 or resseq 260:534)
112chain 'E'
212chain 'F'
312chain 'G'
412chain 'H'

NCS ensembles :
ID
1
2

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Components

#1: Protein
Thioredoxin reductase 2 / TrxR2


Mass: 59752.160 Da / Num. of mol.: 4 / Mutation: C535S
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 (NADPH)
#2: Protein
Thioredoxin / Trx


Mass: 12854.468 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20% PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98696 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98696 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. all: 110173 / Num. obs: 107823 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 56.97 Å2 / Rsym value: 0.109 / Net I/σ(I): 9.35
Reflection shellResolution: 2.37→2.43 Å / Redundancy: 3 % / % possible all: 84.7

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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
Starting model: 3qfb

3qfb


Resolution: 2.371→19.971 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 37.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 7647 7.09 %
Rwork0.2363 --
obs0.2383 107806 98.05 %
all-110173 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.7137 Å2-0 Å2-7.5065 Å2
2---3.8246 Å20 Å2
3---11.5382 Å2
Refinement stepCycle: LAST / Resolution: 2.371→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18840 0 212 215 19267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919432
X-RAY DIFFRACTIONf_angle_d1.20726256
X-RAY DIFFRACTIONf_dihedral_angle_d15.1237128
X-RAY DIFFRACTIONf_chiral_restr0.0792940
X-RAY DIFFRACTIONf_plane_restr0.0043300
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3775X-RAY DIFFRACTIONPOSITIONAL
12B3775X-RAY DIFFRACTIONPOSITIONAL0.049
13C3775X-RAY DIFFRACTIONPOSITIONAL0.046
14D3775X-RAY DIFFRACTIONPOSITIONAL0.038
21E823X-RAY DIFFRACTIONPOSITIONAL
22F823X-RAY DIFFRACTIONPOSITIONAL0.029
23G823X-RAY DIFFRACTIONPOSITIONAL0.031
24H823X-RAY DIFFRACTIONPOSITIONAL0.028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3707-2.39760.42611450.38422279X-RAY DIFFRACTION68
2.3976-2.42570.38942180.33963417X-RAY DIFFRACTION99
2.4257-2.45530.37252170.32823378X-RAY DIFFRACTION99
2.4553-2.48630.314960.33323591X-RAY DIFFRACTION98
2.4863-2.51890.3827190.3433597X-RAY DIFFRACTION100
2.5189-2.55340.4071300.33733598X-RAY DIFFRACTION98
2.5534-2.58980.3658510.32373515X-RAY DIFFRACTION100
2.5898-2.62840.3245650.31653585X-RAY DIFFRACTION99
2.6284-2.66930.3049800.3173543X-RAY DIFFRACTION100
2.6693-2.7130.34211030.30273520X-RAY DIFFRACTION99
2.713-2.75970.33931200.30193506X-RAY DIFFRACTION100
2.7597-2.80970.33451600.31193445X-RAY DIFFRACTION99
2.8097-2.86360.33721920.30223414X-RAY DIFFRACTION100
2.8636-2.92190.3412530.29983414X-RAY DIFFRACTION99
2.9219-2.98520.33463010.29433337X-RAY DIFFRACTION99
2.9852-3.05440.32593300.29613292X-RAY DIFFRACTION100
3.0544-3.13050.28623620.26553274X-RAY DIFFRACTION99
3.1305-3.21480.31934110.26873222X-RAY DIFFRACTION99
3.2148-3.3090.32753720.25663273X-RAY DIFFRACTION99
3.309-3.41530.27733990.25643222X-RAY DIFFRACTION100
3.4153-3.53670.28993740.24973289X-RAY DIFFRACTION99
3.5367-3.67750.27463770.2293240X-RAY DIFFRACTION99
3.6775-3.84370.26764140.21423220X-RAY DIFFRACTION99
3.8437-4.04480.25033900.21023239X-RAY DIFFRACTION99
4.0448-4.29590.22533700.19753266X-RAY DIFFRACTION99
4.2959-4.62380.22553700.18113299X-RAY DIFFRACTION99
4.6238-5.08210.21533760.17233256X-RAY DIFFRACTION99
5.0821-5.80170.24093830.18483295X-RAY DIFFRACTION99
5.8017-7.25090.22713800.19313299X-RAY DIFFRACTION99
7.2509-19.97220.18833790.1673334X-RAY DIFFRACTION98

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