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Yorodumi- PDB-4dvq: Structure of human aldosterone synthase, CYP11B2, in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dvq | ||||||
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Title | Structure of human aldosterone synthase, CYP11B2, in complex with deoxycorticosterone | ||||||
Components | Cytochrome P450 11B2, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / CYP11B2 / Aldosterone synthase / monooxygenase / heme protein / mineralocorticoid / corticosteroid / mitochondria / membrane | ||||||
Function / homology | Function and homology information corticosterone 18-monooxygenase / regulation of blood volume by renal aldosterone / Defective CYP11B2 causes CMO-1 deficiency / mineralocorticoid biosynthetic process / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process ...corticosterone 18-monooxygenase / regulation of blood volume by renal aldosterone / Defective CYP11B2 causes CMO-1 deficiency / mineralocorticoid biosynthetic process / steroid 11beta-monooxygenase / steroid 11-beta-monooxygenase activity / corticosterone 18-monooxygenase activity / cortisol metabolic process / aldosterone biosynthetic process / cortisol biosynthetic process / Mineralocorticoid biosynthesis / glucocorticoid biosynthetic process / Glucocorticoid biosynthesis / sodium ion homeostasis / sterol metabolic process / cellular response to potassium ion / C21-steroid hormone biosynthetic process / potassium ion homeostasis / renal water homeostasis / cellular response to peptide hormone stimulus / steroid hydroxylase activity / Endogenous sterols / cellular response to hormone stimulus / cholesterol metabolic process / mitochondrial inner membrane / iron ion binding / heme binding / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å | ||||||
Authors | Strushkevich, N. / Shen, L. / Tempel, W. / Arrowsmith, C. / Edwards, A. / Usanov, S.A. / Park, H.-W. | ||||||
Citation | Journal: Mol.Endocrinol. / Year: 2013 Title: Structural insights into aldosterone synthase substrate specificity and targeted inhibition. Authors: Strushkevich, N. / Gilep, A.A. / Shen, L. / Arrowsmith, C.H. / Edwards, A.M. / Usanov, S.A. / Park, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dvq.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4dvq.ent.gz | 921.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dvq ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dvq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55649.500 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Aldosterone synthase, CYP11B2 / Plasmid: pCW / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a References: UniProt: P19099, steroid 11beta-monooxygenase, corticosterone 18-monooxygenase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-1CA / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 6% PEG 4000, 0.1M Tris, pH 8.5, 0.2M Lithium sulfate, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→48.55 Å / Num. obs: 245749 / % possible obs: 99.21 % / Redundancy: 4.24 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.7435 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.07 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / SU B: 10.859 / SU ML: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→48.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.56 Å
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