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Yorodumi- PDB-5jsf: Crystal structure of 17beta-hydroxysteroid dehydrogenase 14 S205 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jsf | |||||||||
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Title | Crystal structure of 17beta-hydroxysteroid dehydrogenase 14 S205 variant in complex with NAD. | |||||||||
Components | 17-beta-hydroxysteroid dehydrogenase 14 | |||||||||
Keywords | OXIDOREDUCTASE / cofactor complex / hydroxysteroid dehydrogenase | |||||||||
Function / homology | Function and homology information 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 / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.842 Å | |||||||||
Authors | Bertoletti, N. / Marchais-Oberwinkler, S. / Heine, A. / Klebe, G. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: New Insights into Human 17 beta-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor. Authors: Bertoletti, N. / Braun, F. / Lepage, M. / Moller, G. / Adamski, J. / Heine, A. / Klebe, G. / Marchais-Oberwinkler, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jsf.cif.gz | 117.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jsf.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/5jsf ftp://data.pdbj.org/pub/pdb/validation_reports/js/5jsf | HTTPS FTP |
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-Related structure data
Related structure data | 5hs6C 5icmC 5icsC 5js6C 5en4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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, 1 molecules A
#1: Protein | Mass: 28668.717 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): pLysS References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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-Non-polymers , 5 types, 90 molecules
#2: Chemical | ChemComp-NAD / |
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#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PGE / |
#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.77 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES 0.1 M pH 7.00, sodium formate 3.3 M / PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 31827 / % possible obs: 99.9 % / Redundancy: 6.66 % / Rsym value: 0.047 / Net I/σ(I): 21.35 |
Reflection shell | Resolution: 1.84→1.95 Å / Redundancy: 6.82 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EN4 Resolution: 1.842→46.052 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.842→46.052 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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