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- PDB-4a5l: Crystal structure of the thioredoxin reductase from Entamoeba his... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4a5l | ||||||
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Title | Crystal structure of the thioredoxin reductase from Entamoeba histolytica | ||||||
![]() | THIOREDOXIN REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / REDOX METABOLISM / OXIDATIVE STRESS | ||||||
Function / homology | ![]() thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / nucleotide binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Podust, L.M. | ||||||
![]() | ![]() Title: X-Ray Structures of Thioredoxin and Thioredoxin Reductase from Entamoeba Histolytica and Prevailing Hypothesis of the Mechanism of Auranofin Action. Authors: Parsonage, D. / Sheng, F. / Hirata, K. / Debnath, A. / Mckerrow, J.H. / Reed, S.L. / Abagyan, R. / Poole, L.B. / Podust, L.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152 KB | Display | ![]() |
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PDB format | ![]() | 117.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 49.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a65C ![]() 4cbqC ![]() 4ccqC ![]() 4ccrC ![]() 4cw9C ![]() 4up3C ![]() 3itjS 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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Components
#1: Protein | Mass: 33779.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: C4LW95, thioredoxin-disulfide reductase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NDP): NICOTINAMIDE AND RIBOSE MOIETIES ...NADPH DIHYDRO-NICOTINAMI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.7 % / Description: NONE |
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Crystal grow | pH: 9 Details: 20% PEG 4000, 0.1 M BICINE, PH 9.0, 0.1 M AMMONIUM SULFATE, 0.01 M MG FORMATE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 7, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→103.77 Å / Num. obs: 60309 / % possible obs: 80.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.6 / % possible all: 32.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ITJ Resolution: 1.66→103.76 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.084 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NICOTINAMIDE AND RIBOSE MOIETIES OF NADPH ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.657 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→103.76 Å
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Refine LS restraints |
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