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- PDB-5l92: The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l92 | ||||||
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Title | The 2.1 A crystal structure of CYP109E1 from Bacillus megaterium in complex with corticosterone | ||||||
![]() | Cytochrome P450 | ||||||
![]() | OXIDOREDUCTASE / Bacillus / Bacterial Proteins / Binding Sites / Catalysis / Corticosterone / Cytochrome P-450 Enzyme System / Cytochrome P450 / Hydroxylation / Escherichia coli / Heme / Ligands / Molecular Structure / Oxidation-Reduction / Oxygen / Protein / Protein Structure / Secondary / Steroids / Substrate Specificity | ||||||
Function / homology | ![]() Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / 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 | ![]() ![]() ![]() | ||||||
![]() | Jozwik, I.K. / Thunnissen, A.M.W.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium. Authors: Jozwik, I.K. / Kiss, F.M. / Abdulmughni, A. / Brill, E. / Zapp, J. / Pleiss, J. / Bernhardt, R. / Thunnissen, A.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.4 KB | Display | ![]() |
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PDB format | ![]() | 134.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l90C ![]() 5l91C ![]() 5l94C ![]() 4ggvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47818.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 319 / Gene: BMD_3874 / Production host: ![]() ![]() References: UniProt: D5DKI8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: D5DKI8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor #2: Chemical | #3: Chemical | ChemComp-C0R / | #4: Chemical | ChemComp-MLA / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 9% PEG 3350 and 8% tacsimate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 15, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.1→47.98 Å / Num. obs: 51292 / % possible obs: 97.4 % / Redundancy: 3 % / Biso Wilson estimate: 30.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.022 / Rrim(I) all: 0.04 / Net I/σ(I): 23.3 / Num. measured all: 156293 | |||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GGV Resolution: 2.1→42.766 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.88
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.73 Å2 / Biso mean: 38.5779 Å2 / Biso min: 19.81 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→42.766 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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