[English] 日本語
Yorodumi- PDB-6zdi: 17beta-hydroxysteroid dehydrogenase type 14 variant S205 in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zdi | ||||||
---|---|---|---|---|---|---|---|
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: 2.13 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6zdi.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zdi.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/6zdi ftp://data.pdbj.org/pub/pdb/validation_reports/zd/6zdi | HTTPS FTP |
---|
-Related structure data
Related structure data | 6zraC 5icmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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.) 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 |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
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: 0.9184 Å / Relative weight: 1 |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|