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- PDB-8tay: The crystal structure of T252E CYP199A4 bound to 4-(thiophen-3-yl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tay | ||||||
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Title | The crystal structure of T252E CYP199A4 bound to 4-(thiophen-3-yl)benzoic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / peroxygenase | ||||||
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: Characterisation of the heme aqua-ligand coordination environment in an engineered peroxygenase cytochrome P450 variant. Authors: Podgorski, M.N. / Lee, J.H.Z. / Harbort, J.S. / Nguyen, G.T.H. / Doherty, D.Z. / Donald, W.A. / Harmer, J.R. / Bruning, J.B. / 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 | ![]() | 102.6 KB | Display | ![]() |
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PDB format | ![]() | 73.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tawC ![]() 8tnkC ![]() 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
#1: Protein | Mass: 44615.438 Da / Num. of mol.: 1 / Mutation: T252E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: RPB_3613 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-EJD / |
#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: 2.03 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: The crystallisation 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: Aug 14, 2018 |
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: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→44.082 Å / Num. obs: 23380 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.054 / Rrim(I) all: 0.141 / Χ2: 0.53 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.02→2.07 Å / % possible obs: 89.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.632 / Num. measured all: 8947 / Num. unique obs: 1558 / CC1/2: 0.874 / Rpim(I) all: 0.281 / Rrim(I) all: 0.694 / Χ2: 0.51 / Net I/σ(I) obs: 2.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5uvb Resolution: 2.021→44.082 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.87 / 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: 2.021→44.082 Å
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Refine LS restraints |
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LS refinement shell |
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