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- PDB-7wbc: Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wbc | ||||||
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Title | Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4S)-2-2-methyl-2,4-pentanediol | ||||||
![]() | SDR family NAD(P)-dependent oxidoreductase | ||||||
![]() | OXIDOREDUCTASE / Hydroxysteroid dehydrogenase / Complex / NAD+ | ||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, S.-C. / Zheng, Y.-C. / Xu, J.-H. / Li, C.-X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Hydroxysteroid dehydrogenase wild-type complexed with NAD+ and (4S)-2-2-methyl-2,4-pentanediol Authors: Shi, S.-C. / Zheng, Y.-C. / Xu, J.-H. / Li, C.-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 | ![]() | 118 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jy1S 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 on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 27430.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 346 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-PO4 / | #7: 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: 2.11 Å3/Da / Density % sol: 41.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2-(N-Morpholino) ethane sulfonic acid, MgCl2, CaCl2, MPD, P3350, 2-(N-morpholino) ethane sulfonic acid, imidazole |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2→33.3 Å / Num. obs: 30411 / % possible obs: 95.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 24.42 Å2 / CC1/2: 0.979 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 1560 / CC1/2: 0.978 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JY1 Resolution: 2→33.3 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.4 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.82 Å2 / Biso mean: 26.0029 Å2 / Biso min: 14.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→33.3 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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