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Yorodumi- PDB-3a51: Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by dire... -
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-Basic information
Entry | Database: PDB / ID: 3a51 | ||||||
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Title | Structure of cytochrome P450 Vdh mutant (Vdh-K1) obtained by directed evolution with bound 25-hydroxyvitamin D3 | ||||||
Components | Vitamin D hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / vitamin D3 hydroxylase / hemoprotein / monooxygenase / directed evolution | ||||||
Function / homology | Function and homology information 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 | Pseudonocardia autotrophica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yasutake, Y. / Fujii, Y. / Cheon, W.K. / Arisawa, A. / Tamura, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a51.cif.gz | 429.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a51.ent.gz | 349.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a51_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 3a51_full_validation.pdf.gz | 3.1 MB | Display | |
Data in XML | 3a51_validation.xml.gz | 87.6 KB | Display | |
Data in CIF | 3a51_validation.cif.gz | 123.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/3a51 ftp://data.pdbj.org/pub/pdb/validation_reports/a5/3a51 | HTTPS FTP |
-Related structure data
Related structure data | 3a4gSC 3a4hC 3a4zC 3a50C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Pseudonocardia autotrophica (bacteria) / Strain: NBRC 12743 / Gene: vdh / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4B644 |
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-Non-polymers , 6 types, 1344 molecules
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-VDY / #4: Chemical | ChemComp-CA / #5: Chemical | #6: Chemical | ChemComp-ACT / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M calcium acetate, 10.8% PEG3350, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 1, 2008 |
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→50 Å / Num. obs: 170383 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 3.3 / Num. unique all: 16867 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A4G Resolution: 2→45.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.887 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.156 / 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: 30.419 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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