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Yorodumi- PDB-6zra: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zra | ||||||
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Title | 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in complex with 2-fluoro-5-nitrophenol | ||||||
Components | 17-beta-hydroxysteroid dehydrogenase 14 | ||||||
Keywords | OXIDOREDUCTASE / Inhibitor Complex | ||||||
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: 1.73 Å | ||||||
Authors | Badran, M.J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zra.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zra.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zr/6zra ftp://data.pdbj.org/pub/pdb/validation_reports/zr/6zra | HTTPS FTP |
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-Related structure data
Related structure data | 6zdiC 5icmS 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 / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 28329.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Wild type - S205 variant / Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B14, DHRS10, SDR3, SDR47C1, UNQ502/PRO474 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9BPX1, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor |
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#3: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 134 molecules
#2: Chemical | ChemComp-QFT / |
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#4: Chemical | ChemComp-NAD / |
#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: PEG6000 25% w/v HEPES 0.1M DMSO 2.5% 2-hydroxypropyl-beta-cyclodextrin 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: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→46.2 Å / Num. obs: 29510 / % possible obs: 99.9 % / Redundancy: 15 % / Biso Wilson estimate: 23.44 Å2 / CC1/2: 0.99 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.73→1.83 Å / Redundancy: 13 % / Num. unique obs: 4670 / CC1/2: 0.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ICM Resolution: 1.73→46.2 Å / SU ML: 0.1338 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.1298 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: 25.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→46.2 Å
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Refine LS restraints |
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LS refinement shell |
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