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- PDB-2zby: Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zby | ||||||
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Title | Crystal structure of vitamin D hydroxylase cytochrome P450 105A1 (R84A mutant) | ||||||
![]() | Cytochrome P450-SU1 | ||||||
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Function / homology | ![]() vitamin D 1,25-hydroxylase / vitamin D3 metabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / iron ion binding / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sugimoto, H. / Shinkyo, R. / Hayashi, K. / Yoneda, S. / Yamada, M. / Kamakura, M. / Ikushiro, S. / Shiro, Y. / Sakaki, T. | ||||||
![]() | ![]() Title: Crystal Structure of CYP105A1 (P450SU-1) in Complex with 1alpha,25-Dihydroxyvitamin D3 Authors: Sugimoto, H. / Shinkyo, R. / Hayashi, K. / Yoneda, S. / Yamada, M. / Kamakura, M. / Ikushiro, S. / Shiro, Y. / Sakaki, 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 | ![]() | 102.3 KB | Display | ![]() |
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PDB format | ![]() | 75.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zbxSC ![]() 2zbzC 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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Unit cell |
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Components
#1: Protein | Mass: 44991.742 Da / Num. of mol.: 1 / Mutation: R84A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / ![]() |
#3: Water | ChemComp-HOH / ![]() |
Sequence details | THERE IS A CONFLICT BETWEEN THE SEQUENCES GIVEN IN THE DEPOSITION AND THE DATABASE. ACCORDING TO ...THERE IS A CONFLICT BETWEEN THE SEQUENCES GIVEN IN THE DEPOSITION |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.31 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 20% PEG 8000, 0.1M bis-Tris-propane, 0.2M sodium chloride, 50mM lithium nitrate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2007 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.6→20 Å / Num. obs: 54213 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.004 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5 / Num. unique all: 5192 / Rsym value: 0.329 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2ZBX Resolution: 1.6→19.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.699 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.184 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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