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- PDB-8jbz: 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: 8jbz | ||||||
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Title | Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 4-androstadiene-3,17- dione | ||||||
![]() | 3-ketosteroid dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / 3-ketosteroid delta1-dehydrogenase / Rhodococcus erythropolis SQ1 / 4-androstadiene-3 / 17- dione. | ||||||
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 4-androstadiene-3,17- dione Authors: Hu, Y.L. / Li, X. / Cheng, X.Y. / Song, S.K. / 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 | ![]() | 187.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 28.7 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 on special symmetry positions |
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Components
#1: Protein | Mass: 54253.914 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-ASD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic, 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: 2.079→104.234 Å / Num. obs: 58119 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 1 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.08→2.14 Å / Num. unique obs: 4463 / CC1/2: 0.858 |
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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: 41.679 Å2
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Refinement step | Cycle: LAST / Resolution: 2.079→104.234 Å
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Refine LS restraints |
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LS refinement shell |
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