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- PDB-8vfr: The crystal structure of 4-methylbenzoic acid-bound GALQE CYP199A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8vfr | ||||||
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Title | The crystal structure of 4-methylbenzoic acid-bound GALQE CYP199A4 after soaking in 10 mM H2O2 for 5 minutes | ||||||
![]() | Cytochrome P450![]() | ||||||
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Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Podgorski, M.N. / Bell, S.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Engineering Peroxygenase Activity into Cytochrome P450 Monooxygenases through Modification of the Oxygen Binding Region Authors: Podgorski, M.N. / Akter, J. / Churchman, L.R. / Bruning, J.B. / De Voss, J.J. / Bell, S.G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.7 KB | Display | ![]() |
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PDB format | ![]() | 72.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8vf0C ![]() 8vf3C ![]() 8vfpC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 44628.480 Da / Num. of mol.: 1 / Mutation: A248G, G249A, D251Q, T252E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: RPB_3613 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 272 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/4MA.gif)
![](data/chem/img/E5X.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4MA.gif)
![](data/chem/img/E5X.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / ![]() |
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#3: Chemical | ChemComp-4MA / ![]() |
#4: Chemical | ChemComp-E5X / |
#5: Chemical | ChemComp-CL / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.15 % |
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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2023 |
Radiation | Monochromator: Double-crystal Si(111) liquid nitrogen cooled (DC) or channel-cut Si(111) liquid nitrogen cooled (CC) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.01→44.15 Å / Num. obs: 23259 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.1 / Rrim(I) all: 0.264 / Χ2: 0.49 / Net I/σ(I): 5.4 / Num. measured all: 159873 |
Reflection shell | Resolution: 2.01→2.07 Å / % possible obs: 90.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 1.624 / Num. measured all: 9579 / Num. unique obs: 1562 / CC1/2: 0.553 / Rpim(I) all: 0.703 / Rrim(I) all: 1.774 / Χ2: 0.42 / Net I/σ(I) obs: 0.9 |
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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: 2.018→42.894 Å
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Refine LS restraints |
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LS refinement shell |
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