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Open data
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Basic information
Entry | Database: PDB / ID: 3d21 | ||||||
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Title | Crystal structure of a poplar wild-type thioredoxin h, PtTrxh4 | ||||||
![]() | Thioredoxin H-type | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Koh, C.S. / Didierjean, C. / Corbier, C. / Rouhier, N. / Jacquot, J.P. / Gelhaye, E. | ||||||
![]() | ![]() Title: An Atypical Catalytic Mechanism Involving Three Cysteines of Thioredoxin. Authors: Koh, C.S. / Navrot, N. / Didierjean, C. / Rouhier, N. / Hirasawa, M. / Knaff, D.B. / Wingsle, G. / Samian, R. / Jacquot, J.P. / Corbier, C. / Gelhaye, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.5 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15666.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Plasmid: pSBET / Production host: ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.25 % |
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Crystal grow![]() | Temperature: 293 K / Method: microbatch under oil / pH: 7.5 Details: 0.1 M Na HEPES (pH 7.5), 30 % (w/v) PEG 4000, 0.2 M CaCl2) with 1 mM DTT added to the initial protein solution, microbatch under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 16, 2005 / Details: mirrors |
Radiation | Monochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→50 Å / Num. all: 13453 / Num. obs: 13453 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: SeMet Model solved using SAD method Resolution: 2.15→41 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.664 / SU ML: 0.2 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.534 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.208 Å / Total num. of bins used: 20
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