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Yorodumi- PDB-7x3z: Crystal structure of human 17beta-hydroxysteroid dehydrogenase ty... -
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-Basic information
Entry | Database: PDB / ID: 7x3z | ||||||
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Title | Crystal structure of human 17beta-hydroxysteroid dehydrogenase type 1 complexed with estrone and NAD | ||||||
Components | 17-beta-hydroxysteroid dehydrogenase type 1 | ||||||
Keywords | OXIDOREDUCTASE / 17BETA-HSD1 / ESTRONE / FUNCTIONAL ANALYSES / STEROID / NAD/NADH | ||||||
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 dehydrogenase (NAD+) activity / testosterone biosynthetic process ...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 dehydrogenase (NAD+) activity / testosterone biosynthetic process / 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 / adipose tissue development / catalytic activity / skeletal muscle tissue development / steroid binding / bone development / gene expression / NADP binding / protein homodimerization activity / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Model details | 17beta-HSD1-E1 complex | ||||||
Authors | Li, T. / Lin, S.X. / Yin, H. | ||||||
Funding support | 1items
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Citation | Journal: J.Steroid Biochem.Mol.Biol. / Year: 2023 Title: New insights into the substrate inhibition of human 17 beta-hydroxysteroid dehydrogenase type 1. Authors: Li, T. / Song, X. / Stephen, P. / Yin, H. / 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 | 7x3z.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x3z.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 7x3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/7x3z ftp://data.pdbj.org/pub/pdb/validation_reports/x3/7x3z | HTTPS FTP |
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-Related structure data
Related structure data | 1jtvS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34989.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSD17B1, E17KSR, EDH17B1, EDH17B2, EDHB17, SDR28C1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P14061, 3(or 17)beta-hydroxysteroid dehydrogenase, 17beta-estradiol 17-dehydrogenase #2: Chemical | #3: Chemical | ChemComp-J3Z / ( | #4: Water | ChemComp-HOH / | 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: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: KH2PO4, PEG 8000 / PH range: 7.5-7.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→25 Å / Num. obs: 26759 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.983 / Rpim(I) all: 0.075 / Rrim(I) all: 0.202 / Net I/σ(I): 7.9 / Num. measured all: 196005 |
Reflection shell | Resolution: 2.25→2.37 Å / % possible obs: 100 % / Redundancy: 7.4 % / Num. measured all: 28323 / Num. unique obs: 3824 / CC1/2: 0.932 / Rpim(I) all: 0.185 / Rrim(I) all: 0.509 / Net I/σ(I) obs: 3.4 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.562
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JTV Resolution: 2.25→24.99 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.21 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.441 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→24.99 Å
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