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Yorodumi- PDB-4nkz: Human steroidogenic cytochrome P450 17A1 mutant A105L with substr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nkz | ||||||
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Title | Human steroidogenic cytochrome P450 17A1 mutant A105L with substrate 17alpha-hydroxypregnenolone | ||||||
Components | Steroid 17-alpha-hydroxylase/17,20 lyase | ||||||
Keywords | OXIDOREDUCTASE / LYASE / heme protein / monooxygenase / steroid 17alpha-hydroxylase / steroid C17 / 20 lyase / NADPH-cytochrome P450 reductase / cytochrome b5 / endoplasmic reticulum membrane | ||||||
Function / homology | Function and homology information Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process ...Defective CYP17A1 causes AH5 / steroid 17alpha-monooxygenase / 17alpha-hydroxyprogesterone deacetylase / steroid 17-alpha-monooxygenase activity / : / glucocorticoid biosynthetic process / Androgen biosynthesis / hormone biosynthetic process / Glucocorticoid biosynthesis / androgen biosynthetic process / sex differentiation / progesterone metabolic process / steroid biosynthetic process / steroid metabolic process / oxygen binding / iron ion binding / axon / neuronal cell body / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å | ||||||
Authors | Scott, E.E. / Petrunak, E.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structures of Human Steroidogenic Cytochrome P450 17A1 with Substrates. Authors: Petrunak, E.M. / DeVore, N.M. / Porubsky, P.R. / Scott, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nkz.cif.gz | 704 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nkz.ent.gz | 596 KB | Display | PDB format |
PDBx/mmJSON format | 4nkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nkz_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 4nkz_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 4nkz_validation.xml.gz | 63.8 KB | Display | |
Data in CIF | 4nkz_validation.cif.gz | 84.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/4nkz ftp://data.pdbj.org/pub/pdb/validation_reports/nk/4nkz | HTTPS FTP |
-Related structure data
Related structure data | 4nkvC 4nkwC 4nkxC 4nkyC 3swzS 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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Unit cell |
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-Components
#1: Protein | Mass: 55782.223 Da / Num. of mol.: 4 / Fragment: UNP residues 24-508 / Mutation: A105L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP17, CYP17A1, S17AH / Plasmid: pCWori17A1delta19H / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P05093, EC: 1.14.99.9, EC: 4.1.2.30 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-LZZ / ( #4: 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: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris-HCl, 150 mM magnesium chloride hexahydrate, 25% PEG4000, 6% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013 / Details: Rh coated mirror, K-B focusing mirror |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→38.7 Å / Num. obs: 44496 / % possible obs: 98.9 % / Redundancy: 6.5 % |
Reflection shell | Resolution: 3→3.17 Å / Redundancy: 6 % / % possible all: 94.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SWZ Resolution: 3.003→38.695 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 31.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.003→38.695 Å
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Refine LS restraints |
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LS refinement shell |
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