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- PDB-7tru: The crystal structure of WT CYP199A4 bound to 4-(thiophen-2-yl)be... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tru | ||||||
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Title | The crystal structure of WT CYP199A4 bound to 4-(thiophen-2-yl)benzoic acid | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / thiophene 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.N. / Bell, S.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes. Authors: Podgorski, M.N. / Keto, A.B. / Coleman, T. / 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 | ![]() | 110.5 KB | Display | ![]() |
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PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7trtC ![]() 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: 44587.430 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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#2: Chemical | ChemComp-KQR / |
#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: 2.04 Å3/Da / Density % sol: 39.57 % |
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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: Oct 3, 2020 | |||||||||||||||||||||||||||
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: 0.95372 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.45→44.27 Å / Num. obs: 62810 / % possible obs: 99.5 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.046 / Rrim(I) all: 0.121 / Net I/σ(I): 9.4 / Num. measured all: 425297 / Scaling rejects: 598 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.4 %
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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: 5UVB Resolution: 1.454→39.712 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.26 / 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: 88.43 Å2 / Biso mean: 18.7557 Å2 / Biso min: 7.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.454→39.712 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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