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- PDB-3b99: Crystal structure of zebrafish prostacyclin synthase (cytochrome ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3b99 | ||||||
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Title | Crystal structure of zebrafish prostacyclin synthase (cytochrome P450 8A1) in complex with substrate analog U51605 | ||||||
![]() | Prostaglandin I2 synthase | ||||||
![]() | ISOMERASE / prostacyclin synthase / cytochrome p450 8A1 / CYP8A1 / substrate analog-enzyme complex | ||||||
Function / homology | ![]() Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nicotinamide salvaging / Eicosanoids / Sterols are 12-hydroxylated by CYP8B1 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-I synthase / prostaglandin-I synthase activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / hydroperoxy icosatetraenoate dehydratase ...Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Nicotinamide salvaging / Eicosanoids / Sterols are 12-hydroxylated by CYP8B1 / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin-I synthase / prostaglandin-I synthase activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / hydroperoxy icosatetraenoate dehydratase / hydroperoxy icosatetraenoate dehydratase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / prostaglandin biosynthetic process / monooxygenase activity / iron ion binding / heme binding / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, Y.-C. / Chiang, C.-W. / Yeh, H.-C. / Hsu, P.-Y. / Whitby, F.G. / Wang, L.-H. / Chan, N.-L. | ||||||
![]() | ![]() Title: Structures of Prostacyclin Synthase and Its Complexes with Substrate Analog and Inhibitor Reveal a Ligand-specific Heme Conformation Change Authors: Li, Y.-C. / Chiang, C.-W. / Yeh, H.-C. / Hsu, P.-Y. / Whitby, F.G. / Wang, L.-H. / Chan, N.-L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.7 KB | Display | ![]() |
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PDB format | ![]() | 156.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 36.2 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b6hC ![]() 3b98C ![]() 2iagS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 54848.930 Da / Num. of mol.: 2 / Fragment: UNP residues 17-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A9LLA5, UniProt: F1RE08*PLUS, prostaglandin-I synthase #2: Chemical | #3: Chemical | ChemComp-U51 / ( #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.86 % |
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Crystal grow | Temperature: 277 K / Method: soaking / pH: 7.5 Details: The crystal of prostacyclin synthase-U51605 complex was prepared by soaking the ligand-free crystals in 2 microliter of substitute mother liquor (23% PEG 3350, 50mM HEPES (Na-salt; pH 7.5)) ...Details: The crystal of prostacyclin synthase-U51605 complex was prepared by soaking the ligand-free crystals in 2 microliter of substitute mother liquor (23% PEG 3350, 50mM HEPES (Na-salt; pH 7.5)) containing 0.25mM of U51605 for a week, Soaking, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2007 / Details: Toroidal FM |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 35343 / Num. obs: 32622 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rsym value: 0.064 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3269 / Rsym value: 0.302 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2IAG Resolution: 2.5→27.75 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.865 / SU B: 10.747 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 1.415 / ESU R Free: 0.373 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.075 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→27.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.482→2.546 Å / Total num. of bins used: 20
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