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- PDB-7tp5: The crystal structure of T252E CYP199A4 bound to 4-ethylthiobenzo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tp5 | ||||||
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Title | The crystal structure of T252E CYP199A4 bound to 4-ethylthiobenzoic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / peroxygenase / sulfoxidation | ||||||
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. / Bell, S.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Investigating the Active Oxidants Involved in Cytochrome P450 Catalyzed Sulfoxidation Reactions. Authors: Podgorski, M.N. / Coleman, T. / Churchman, L.R. / Bruning, J.B. / De Voss, J.J. / 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 | ![]() | 105 KB | Display | ![]() |
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PDB format | ![]() | 74.9 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 | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7tp6C ![]() 7tqmC ![]() 8dybC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44615.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HaA2 / Gene: RPB_3613 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 401 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/81M.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/81M.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||
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#3: Chemical | ChemComp-81M / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-MG / | ||
#6: Chemical | #7: 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: 1.87 Å3/Da / Density % sol: 34.23 % |
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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: 5.0-5.75 |
-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: Jul 5, 2018 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.655→40.7 Å / Num. obs: 31873 / % possible obs: 81.1 % / Redundancy: 5 % / Biso Wilson estimate: 13.11 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.067 / Rrim(I) all: 0.161 / Net I/σ(I): 9.3 | ||||||||||||||||||||||||||||||
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: 1.655→40.697 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / 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: 70.18 Å2 / Biso mean: 16.5554 Å2 / Biso min: 5.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.655→40.697 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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