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- PDB-5nyl: Crystal structure of an atypical poplar thioredoxin-like2.1 activ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nyl | |||||||||
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Title | Crystal structure of an atypical poplar thioredoxin-like2.1 active site mutant | |||||||||
![]() | Thioredoxin-like protein 2.1 | |||||||||
![]() | OXIDOREDUCTASE / atypical thioredoin / disulfide exchange | |||||||||
Function / homology | Thioredoxin-like 3-1/3-2 / Thioredoxin / chloroplast stroma / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / 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 | ![]() | 105.8 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422 KB | Display | ![]() |
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Full document | ![]() | 422.9 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 18.2 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14058.568 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET3d / Details (production host): T7 expression strain / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Na3 citrate, 20%(w/v) 2-propanol, 20%(w/v) PEG 4K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.38 Å / Num. obs: 32801 / % possible obs: 98 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.039 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2 / Num. unique obs: 1377 / CC1/2: 0.719 / Rpim(I) all: 0.41 / % possible all: 83.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: wild-type atypical trx-like2.1 Resolution: 1.5→33.38 Å / Cor.coef. Fo:Fc: 0.9571 / Cor.coef. Fo:Fc free: 0.9434 / SU R Cruickshank DPI: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.079
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Displacement parameters | Biso mean: 20.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.188 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→33.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Total num. of bins used: 16
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