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Yorodumi- PDB-5jkw: HUMAN PLACENTAL AROMATASE CYTOCHROME P450 (CYP19A1) COMPLEXED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jkw | ||||||
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Title | HUMAN PLACENTAL AROMATASE CYTOCHROME P450 (CYP19A1) COMPLEXED WITH TESTOSTERONE | ||||||
Components | Aromatase | ||||||
Keywords | OXIDOREDUCTASE / Aromatase / cytochrome P450 / human placenta / estrogen synthase / testosterone | ||||||
Function / homology | Function and homology information aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / negative regulation of chronic inflammatory response / estrogen biosynthetic process / Estrogen biosynthesis / testosterone biosynthetic process ...aromatase / Defective CYP19A1 causes AEXS / positive regulation of estradiol secretion / androgen catabolic process / female genitalia development / syncytium formation / negative regulation of chronic inflammatory response / estrogen biosynthetic process / Estrogen biosynthesis / testosterone biosynthetic process / sterol metabolic process / prostate gland growth / mammary gland development / negative regulation of macrophage chemotaxis / steroid biosynthetic process / 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 / steroid hydroxylase activity / Endogenous sterols / oxygen binding / response to estradiol / electron transfer activity / iron ion binding / endoplasmic reticulum membrane / heme binding / endoplasmic reticulum / membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Ghosh, D. / Egbuta, C. / Lo, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Steroid Biochem. Mol. Biol. / Year: 2018 Title: Testosterone complex and non-steroidal ligands of human aromatase. Authors: Ghosh, D. / Egbuta, C. / Lo, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jkw.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jkw.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 5jkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jkw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5jkw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5jkw_validation.xml.gz | 18 KB | Display | |
Data in CIF | 5jkw_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/5jkw ftp://data.pdbj.org/pub/pdb/validation_reports/jk/5jkw | HTTPS FTP |
-Related structure data
Related structure data | 5jkvC 5jl6C 5jl7C 5jl9C 3s79S 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: 57954.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P11511, aromatase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-TES / |
#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: 5.83 Å3/Da / Density % sol: 78.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 20-30% PEG 4000, PHOSPHATE BUFFER, PH 7.4 |
-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: Dec 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3→30.5 Å / Num. obs: 24964 / % possible obs: 95.7 % / Redundancy: 3.6 % / Net I/σ(I): 23.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3S79 Resolution: 3→30.5 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.638 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.266 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.892 Å2
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Refinement step | Cycle: 1 / Resolution: 3→30.5 Å
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Refine LS restraints |
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