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- PDB-6zdi: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zdi | ||||||
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Title | 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 2-fluoro-5-nitrophenol | ||||||
![]() | 17-beta-hydroxysteroid dehydrogenase 14 | ||||||
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Function / homology | ![]() Estrogen biosynthesis / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)] activity / steroid catabolic process / identical protein binding / ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Badran, M.J. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 2-fluoro-5-nitrophenol Authors: Badran, M.J. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zraC ![]() 5icmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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
#1: Protein | Mass: 28329.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Wild type S205 / Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: Q9BPX1, ![]() |
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#2: Chemical | ChemComp-NAD / ![]() |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-QFT / |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: PEG6000 27% w/v HEPES 1M DMSO 2.5% 2-hydroxypropyl-betaczclodextrin 5mM PH range: 6.5 - 7.5 |
-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: Jan 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.13→50 Å / Num. obs: 16003 / % possible obs: 99.3 % / Redundancy: 8 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 0.99 / Net I/σ(I): 14.47 |
Reflection shell | Resolution: 2.13→2.26 Å / Num. unique obs: 2517 / CC1/2: 0.94 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5ICM Resolution: 2.13→46.34 Å / SU ML: 0.2703 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.2045 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 29.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→46.34 Å
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Refine LS restraints |
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LS refinement shell |
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