+Open data
-Basic information
Entry | Database: PDB / ID: 4kq8 | ||||||
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Title | Structure of Recombinant Human Cytochrome P450 Aromatase | ||||||
Components | Cytochrome P450 19A1 | ||||||
Keywords | OXIDOREDUCTASE / Aromatase / androgen / estrogen / cytochrome P450 / Estrogen synthetase / Cytochrome P450 reductase | ||||||
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 / FOURIER SYNTHESIS / Resolution: 3.29 Å | ||||||
Authors | Ghosh, D. / Di Nardo, G. / Griswold, J. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural basis for the functional roles of critical residues in human cytochrome p450 aromatase. Authors: Lo, J. / Di Nardo, G. / Griswold, J. / Egbuta, C. / Jiang, W. / Gilardi, G. / Ghosh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kq8.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kq8.ent.gz | 79.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/4kq8 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/4kq8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 54685.902 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 | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.1 Å3/Da / Density % sol: 79.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.4 Details: Crystallized from 24%-30% PEG4000, 0.5 M NaCl, 0.05M Tris-HCl and vapor diffused in sealed 24-well sitting drop plates. Crystals appeared after 1-6 week of initial set-up and continued to ...Details: Crystallized from 24%-30% PEG4000, 0.5 M NaCl, 0.05M Tris-HCl and vapor diffused in sealed 24-well sitting drop plates. Crystals appeared after 1-6 week of initial set-up and continued to grow for an additional 2 to 6 weeks after first appearance, pH 7.4, VAPOR DIFFUSION, temperature 277K |
-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 18, 2009 |
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: 3.29→121.95 Å / Num. all: 20153 / Num. obs: 19096 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 98.8 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.29→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9 / SU B: 16.3 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.688 / ESU R Free: 0.37 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.468 Å2
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Refinement step | Cycle: LAST / Resolution: 3.29→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.29→3.379 Å / Total num. of bins used: 20
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