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- PDB-7y9p: Xylitol dehydrogenase S96C/S99C/Y102C mutant(thermostabilized for... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7y9p | ||||||
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Title | Xylitol dehydrogenase S96C/S99C/Y102C mutant(thermostabilized form) from Pichia stipitis | ||||||
![]() | Xylitol dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Xylitol / Medium chain dehydrogenase/reductase family / structural zinc atom | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshiwara, K. / Watanabe, Y. / Watanabe, S. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular evolutionary insight of structural zinc atom in yeast xylitol dehydrogenases and its application in bioethanol production by lignocellulosic biomass. Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.8 KB | Display | ![]() |
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PDB format | ![]() | 59.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qe3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39809.336 Da / Num. of mol.: 1 / Mutation: S96C, S99C, Y102C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 20 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.0, 2.5%(w/v) PEG400, 2.0 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→47.35 Å / Num. obs: 22638 / % possible obs: 100 % / Redundancy: 57.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.457 / Rpim(I) all: 0.061 / Rrim(I) all: 0.461 / Χ2: 1 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 60.5 % / Rmerge(I) obs: 4.19 / Num. measured all: 106523 / Num. unique obs: 1762 / CC1/2: 0.856 / Rpim(I) all: 0.544 / Rrim(I) all: 4.226 / Χ2: 0.98 / Net I/σ(I) obs: 2.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QE3 Resolution: 2.8→47.35 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.71 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→47.35 Å
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Refine LS restraints |
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LS refinement shell |
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