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- PDB-7tnf: The crystal structure of F298V CYP199A4 bound to 4-phenylbenzoic acid -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tnf | ||||||
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Title | The crystal structure of F298V CYP199A4 bound to 4-phenylbenzoic acid | ||||||
![]() | Cytochrome P450![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Podgorski, M. / Bell, S.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Enabling Aromatic Hydroxylation in a Cytochrome P450 Monooxygenase Enzyme through Protein Engineering. Authors: Coleman, T. / Lee, J.Z.H. / Kirk, A.M. / Doherty, D.Z. / Podgorski, M.N. / Pinidiya, D.K. / Bruning, J.B. / De Voss, J.J. / Krenske, E.H. / 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 | ![]() | 109 KB | Display | ![]() |
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PDB format | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7jxbC ![]() 7tndC ![]() 7tnuC ![]() 8d39C ![]() 5uvbS S: Starting model for refinement 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: 44539.387 Da / Num. of mol.: 1 / Mutation: F298V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: HaA2 / Gene: RPB_3613 / Production host: ![]() ![]() ![]() |
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-Non-polymers , 5 types, 512 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/Z7Z.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/Z7Z.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / ![]() |
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#3: Chemical | ChemComp-Z7Z / |
#4: Chemical | ChemComp-CL / ![]() |
#5: Chemical | ChemComp-MG / |
#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: 2.01 Å3/Da / Density % sol: 38.84 % |
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Crystal grow![]() | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 100 mM Bis-Tris (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate, 20-32% PEG3350 PH range: 5.00-5.75 |
-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: Apr 29, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.539→44.25 Å / Num. obs: 52141 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 14.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 11.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 5UVB Resolution: 1.539→39.437 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.19 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 77.75 Å2 / Biso mean: 19.3285 Å2 / Biso min: 9.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.539→39.437 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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