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- PDB-8joj: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhod... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8joj | ||||||
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Title | Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate | ||||||
![]() | 3-ketosteroid dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / 3-ketosteroid delta1-dehydrogenase / Rhodococcus erythropolis SQ1 / 9 / 11-epoxy-17-hydroxypregn-4-ene-3 / 20-dione actate | ||||||
Function / homology | ![]() 3-oxosteroid 1-dehydrogenase activity / steroid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, Y.L. / Li, X. / Cheng, X.Y. / Song, S.K. / Su, Z.D. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate Authors: Song, S.K. / Hu, Y.L. / Li, X. / Su, Z.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186 KB | Display | ![]() |
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PDB format | ![]() | 147.3 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 | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54651.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-UU0 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.43 Å3/Da / Density % sol: 72.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: UPH2O,3.5M Sodium formate pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 3, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.819→103.58 Å / Num. obs: 22365 / % possible obs: 95.7 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.82→2.97 Å / Rmerge(I) obs: 1.341 / Num. unique obs: 3357 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.51 Å2
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Refinement step | Cycle: LAST / Resolution: 2.819→77.764 Å
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Refine LS restraints |
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LS refinement shell |
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