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- PDB-3a4z: Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by dire... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a4z | ||||||
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Title | Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution | ||||||
![]() | Vitamin D hydroxylase | ||||||
![]() | OXIDOREDUCTASE / Cytochrome P450 / vitamin D3 hydroxylase / hemoprotein / monooxygenase / directed evolution | ||||||
Function / homology | ![]() cholestanetriol 26-monooxygenase / : / cholestanetetraol 26-dehydrogenase activity / : / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yasutake, Y. / Fujii, Y. / Cheon, W.K. / Arisawa, A. / Tamura, T. | ||||||
![]() | ![]() Title: Structural evidence for enhancement of sequential vitamin D3 hydroxylation activities by directed evolution of cytochrome P450 vitamin D3 hydroxylase Authors: Yasutake, Y. / Fujii, Y. / Nishioka, T. / Cheon, W.K. / Arisawa, A. / Tamura, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 409.5 KB | Display | ![]() |
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PDB format | ![]() | 334.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 79.2 KB | Display | |
Data in CIF | ![]() | 108.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a4gSC ![]() 3a4hC ![]() 3a50C ![]() 3a51C 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 45587.887 Da / Num. of mol.: 5 / Mutation: T70R, V156L, E216M, E384R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 833 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ACT / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M calcium acetate, 13% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2009 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 129009 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 26 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.86 / Num. unique all: 6327 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3A4G Resolution: 2.2→49.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.627 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.202→2.259 Å / Total num. of bins used: 20
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