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Open data
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Basic information
Entry | Database: PDB / ID: 5hr0 | ||||||
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Title | Crystal structure of thioredoxin E101G mutant | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE / E. coli thioredoxin / thiol-redox reactions | ||||||
Function / homology | ![]() DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Noguera, M.E. / Vazquez, D.S. / Howard, E.I. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J. | ||||||
![]() | ![]() Title: Structural variability of E. coli thioredoxin captured in the crystal structures of single-point mutants. Authors: Noguera, M.E. / Vazquez, D.S. / Ferrer-Sueta, G. / Agudelo, W.A. / Howard, E. / Rasia, R.M. / Manta, B. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.6 KB | Display | ![]() |
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PDB format | ![]() | 126 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.1 KB | Display | ![]() |
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Full document | ![]() | 432 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hr1C ![]() 5hr2C ![]() 5hr3C ![]() 2trxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 11746.521 Da / Num. of mol.: 2 / Mutation: E101G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: The drop was a 1:1 mix of protein (18 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 15 % ethanol, pH 4.75) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.31→19.862 Å / Num. obs: 57845 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 15.64 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.043 / Net I/σ(I): 17 / Num. measured all: 588774 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2TRX Resolution: 1.31→19.862 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / Phase error: 18.96 / 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 | Biso max: 66.62 Å2 / Biso mean: 22.3423 Å2 / Biso min: 9.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.31→19.862 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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