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Open data
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Basic information
Entry | Database: PDB / ID: 4i8b | ||||||
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Title | Crystal Structure of Thioredoxin from Schistosoma Japonicum | ||||||
![]() | Thioredoxin | ||||||
![]() | OXIDOREDUCTASE / thioredoxin fold / protein-disulfide reductase | ||||||
Function / homology | ![]() glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, Q. / Peng, Y. / Zhao, J. / Li, X. / Fan, X. / Zhou, X. / Chen, J. / Luo, Z. / Shi, D. | ||||||
![]() | ![]() Title: Expression, characterization and crystal structure of thioredoxin from Schistosoma japonicum. Authors: Li, Y. / Li, P. / Peng, Y. / Wu, Q. / Huang, F. / Liu, X. / Li, X. / Zhou, H. / Guo, D. / Shi, D. / Zhou, X.N. / Fan, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.6 KB | Display | ![]() |
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PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.3 KB | Display | ![]() |
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Full document | ![]() | 431.4 KB | Display | |
Data in XML | ![]() | 11.3 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 11737.380 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 3350, 50 mM Bistris pH 6.5 and 10 mM BaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9707 Å / Relative weight: 1 |
Reflection | Resolution: 1.996→37.34 Å / Num. all: 18886 / Num. obs: 18886 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 7.9 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.722 / Rsym value: 0.111 / Net I/σ(I): 411.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.745 Å2 / ksol: 0.355 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→37.34 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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