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Yorodumi- PDB-1jtv: Crystal structure of 17beta-Hydroxysteroid Dehydrogenase Type 1 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jtv | ||||||
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Title | Crystal structure of 17beta-Hydroxysteroid Dehydrogenase Type 1 complexed with Testosterone | ||||||
Components | 17 beta-hydroxysteroid dehydrogenase type 1 | ||||||
Keywords | OXIDOREDUCTASE / steroid hormones / alternative binding mode | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å | ||||||
Authors | Shi, R. / Nahoum, V. / Lin, S.X. | ||||||
Citation | Journal: FASEB J. / Year: 2003 Title: Pseudo-symmetry of C19 steroids, alternative binding orientations, and multispecificity in human estrogenic 17beta-hydroxysteroid dehydrogenase. Authors: Gangloff, A. / Shi, R. / Nahoum, V. / 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 | 1jtv.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jtv.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 1jtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jtv_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 1jtv_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 1jtv_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1jtv_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jtv ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jtv | HTTPS FTP |
-Related structure data
Related structure data | 1iolS S: Starting model for refinement |
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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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Details | The second part of the biological assembly is generated by the two fold crystallographic axis |
-Components
#1: Protein | Mass: 34887.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: placenta References: UniProt: P14061, 17beta-estradiol 17-dehydrogenase |
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#2: Chemical | ChemComp-TES / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.3 Å3/Da / Density % sol: 46.61 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / pH: 7.5 Details: PEG 4000,magnesium chloride,beta-octylglucoside,glycerol,Hepes,soaking with testosterone, pH 7.5, temperature 300K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 27 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→40 Å / Num. all: 148865 / Num. obs: 46122 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.54→1.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / Num. unique all: 4586 / % possible all: 99.4 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 148865 |
Reflection shell | *PLUS % possible obs: 99.4 % / Num. unique obs: 4586 / Num. measured obs: 13768 / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1IOL Resolution: 1.54→13.9 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→13.9 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.54 Å / Lowest resolution: 1.6 Å / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.284 |