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Yorodumi- PDB-3dhe: ESTROGENIC 17-BETA HYDROXYSTEROID DEHYDROGENASE COMPLEXED DEHYDRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dhe | ||||||
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Title | ESTROGENIC 17-BETA HYDROXYSTEROID DEHYDROGENASE COMPLEXED DEHYDROEPIANDROSTERONE | ||||||
Components | ESTROGENIC 17-BETA HYDROXYSTEROID DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE / STEROID / DEHYDROEPIANDROSTERONE / DHEA / ANDROGEN | ||||||
Function / homology | Function and homology information estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity ...estradiol binding / 3(or 17)beta-hydroxysteroid dehydrogenase / 17-beta-hydroxysteroid dehydrogenase (NADP+) activity / estrogen biosynthetic process / testosterone dehydrogenase [NAD(P)+] activity / cellular response to metal ion / Estrogen biosynthesis / dihydrotestosterone 17-beta-dehydrogenase activity / testosterone biosynthetic process / testosterone dehydrogenase (NAD+) activity / testosterone 17-beta-dehydrogenase (NADP+) activity / 17beta-estradiol 17-dehydrogenase / estradiol 17-beta-dehydrogenase [NAD(P)+] activity / steroid biosynthetic process / estrogen metabolic process / NADP+ binding / lysosome organization / The canonical retinoid cycle in rods (twilight vision) / small molecule binding / catalytic activity / adipose tissue development / skeletal muscle tissue development / steroid binding / bone development / NADP binding / gene expression / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.3 Å | ||||||
Authors | Han, Q. / Campbell, R.L. / Gangloff, A. / Lin, S.X. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Dehydroepiandrosterone and dihydrotestosterone recognition by human estrogenic 17beta-hydroxysteroid dehydrogenase. C-18/c-19 steroid discrimination and enzyme-induced strain. Authors: Han, Q. / Campbell, R.L. / Gangloff, A. / Huang, Y.W. / Lin, S.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dhe.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dhe.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dhe_validation.pdf.gz | 441.4 KB | Display | wwPDB validaton report |
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Full document | 3dhe_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 3dhe_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3dhe_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dhe ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dhe | HTTPS FTP |
-Related structure data
Related structure data | 1dhtC 1iolS 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
#1: Protein | Mass: 34887.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: PLACENTA References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase |
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#2: Chemical | ChemComp-AND / |
#3: 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: 2.43 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.20 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU R-AXIS II / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→8 Å / Num. obs: 14316 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 86 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Num. measured all: 25462 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1IOL Resolution: 2.3→8 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.3 Å / Total num. of bins used: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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