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- PDB-8vl0: The crystal structure of wild-type CYP199A4 bound to 4-(2-oxoprop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vl0 | ||||||
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Title | The crystal structure of wild-type CYP199A4 bound to 4-(2-oxopropyl)benzoic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / cytochrome P450 / 4-(2-oxopropyl)benzoic acid | ||||||
Function / homology | ![]() cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Podgorski, M.N. / Bell, S.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of wild-type CYP199A4 bound to 4-(2-oxopropyl)benzoic acid Authors: Podgorski, M.N. / Bell, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.1 KB | Display | ![]() |
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PDB format | ![]() | 74 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 30.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44587.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: RPB_3613 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-LVC / Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O3 / Feature type: SUBJECT OF INVESTIGATION |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.62 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350 PH range: 5.0-5.75 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2020 |
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→43.13 Å / Num. obs: 29073 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.068 / Rrim(I) all: 0.176 / Χ2: 0.54 / Net I/σ(I): 7 / Num. measured all: 190714 |
Reflection shell | Resolution: 1.83→1.87 Å / % possible obs: 83.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.911 / Num. measured all: 8639 / Num. unique obs: 1497 / CC1/2: 0.351 / Rpim(I) all: 0.857 / Rrim(I) all: 2.102 / Χ2: 0.45 / Net I/σ(I) obs: 0.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.837→43.128 Å
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Refine LS restraints |
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LS refinement shell |
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