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Yorodumi- PDB-3s79: Human placental aromatase cytochrome P450 (CYP19A1) refined at 2.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s79 | ||||||
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Title | Human placental aromatase cytochrome P450 (CYP19A1) refined at 2.75 angstrom | ||||||
Components | Cytochrome P450 19A1 | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process ...aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / estrogen biosynthetic process / negative regulation of chronic inflammatory response / Estrogen biosynthesis / testosterone biosynthetic process / sterol metabolic process / prostate gland growth / negative regulation of macrophage chemotaxis / mammary gland development / steroid biosynthetic process / steroid hydroxylase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / aromatase activity / female gonad development / uterus development / Endogenous sterols / oxygen binding / response to estradiol / electron transfer activity / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Refinement at higher resolution / Resolution: 2.75 Å | ||||||
Authors | Ghosh, D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Novel aromatase inhibitors by structure-guided design. Authors: Ghosh, D. / Lo, J. / Morton, D. / Valette, D. / Xi, J. / Griswold, J. / Hubbell, S. / Egbuta, C. / Jiang, W. / An, J. / Davies, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s79.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s79.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 3s79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/3s79 ftp://data.pdbj.org/pub/pdb/validation_reports/s7/3s79 | HTTPS FTP |
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-Related structure data
Related structure data | 3s7sC 4gl5C 4gl7C 3eqmS C: citing same article (ref.) 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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-Components
#1: Protein | Mass: 57954.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP19A1, ARO1, CYAR, CYP19 / Production host: Escherichia coli (E. coli) / References: UniProt: P11511, unspecific monooxygenase | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-ASD / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20-30% PEG 4000, phosphate buffer, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2007 | |||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→121.43 Å / Num. all: 33618 / Num. obs: 33618 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 83.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.42 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: Refinement at higher resolution Starting model: PDB ENTRY 3EQM Resolution: 2.75→121.27 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.232 / SU ML: 0.177 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.222 / 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: 69.152 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→121.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.818 Å / Total num. of bins used: 20
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