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- PDB-5nyn: Crystal structure of the atypical poplar thioredoxin-like2.1 in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nyn | |||||||||
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Title | Crystal structure of the atypical poplar thioredoxin-like2.1 in complex with gluathione | |||||||||
![]() | Thioredoxin-like protein 2.1 | |||||||||
![]() | OXIDOREDUCTASE / atypical thioredoxin / disulfide exchange | |||||||||
Function / homology | Thioredoxin-like 3-1/3-2 / Thioredoxin / chloroplast stroma / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / GLUTATHIONE / Thioredoxin-like protein 2.1![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chibani, K. / Saul, F.A. / Haouz, A. / Rouhier, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural snapshots along the reaction mechanism of the atypical poplar thioredoxin-like2.1. Authors: Chibani, K. / Saul, F. / Didierjean, C. / Rouhier, N. / Haouz, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.5 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.1 KB | Display | ![]() |
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Full document | ![]() | 802.1 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14190.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET3d / Details (production host): T7 expression system / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GSH / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Na acetate, 0.2M lithium sulfate, 0.1M hepes7.5, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.7 Å / Num. obs: 19810 / % possible obs: 99.5 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.039 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2 / Num. unique obs: 984 / CC1/2: 0.694 / Rpim(I) all: 0.548 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 23.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.182 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→16.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.69 Å / Total num. of bins used: 10
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