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- PDB-4j56: Structure of Plasmodium falciparum thioredoxin reductase-thioredo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j56 | ||||||
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Title | Structure of Plasmodium falciparum thioredoxin reductase-thioredoxin complex | ||||||
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![]() | OXIDOREDUCTASE / Protein-Protein Complex / Thioredoxin fold / Disulfide reductase / FAD binding / NADPH binding / Thioredoxin binding | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fritz-Wolf, K. / Jortzik, E. / Stumpf, M. / Preuss, J. / Iozef, R. / Rahlfs, S. / Becker, K. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 477.8 KB | Display | ![]() |
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PDB format | ![]() | 391.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 85.6 KB | Display | |
Data in CIF | ![]() | 116.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4j57C ![]() 3qfbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 59752.160 Da / Num. of mol.: 4 / Mutation: C535S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Gene: trxr2, PFI1170c / Plasmid: pRSETa / Production host: ![]() ![]() References: UniProt: P61076, thioredoxin-disulfide reductase #2: Protein | Mass: 12854.468 Da / Num. of mol.: 4 / Mutation: C33S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Gene: PF14_0545 / Plasmid: pQE30 / Production host: ![]() ![]() #3: Chemical | ChemComp-FAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 20% PEG 8000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98696 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.37→2.43 Å / Redundancy: 3 % / % possible all: 84.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3qfb Resolution: 2.371→19.971 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 37.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.371→19.971 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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