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- PDB-5b09: Polyketide cyclase OAC from Cannabis sativa bound with Olivetolic acid -
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Open data
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Basic information
Entry | Database: PDB / ID: 5b09 | ||||||
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Title | Polyketide cyclase OAC from Cannabis sativa bound with Olivetolic acid | ||||||
![]() | Olivetolic acid cyclase | ||||||
![]() | LYASE / Cannabis sativa / plant polyketide cyclase | ||||||
Function / homology | ![]() olivetolic acid cyclase / olivetolic acid biosynthetic process / cannabinoid biosynthetic process / pollen tube adhesion / cyclase activity / terpenoid biosynthetic process / lyase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Yang, X. / Matsui, T. / Mori, T. / Abe, I. / Morita, H. | ||||||
![]() | ![]() Title: Structural basis for olivetolic acid formation by a polyketide cyclase from Cannabis sativa Authors: Yang, X. / Matsui, T. / Kodama, T. / Mori, T. / Zhou, X. / Taura, F. / Noguchi, H. / Abe, I. / Morita, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.3 KB | Display | ![]() |
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PDB format | ![]() | 22.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.9 KB | Display | ![]() |
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Full document | ![]() | 432.9 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b08SC ![]() 5b0aC ![]() 5b0bC ![]() 5b0cC ![]() 5b0dC ![]() 5b0eC ![]() 5b0fC ![]() 5b0gC 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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Unit cell |
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Components
#1: Protein | Mass: 12230.011 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-4MX / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.98 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 100mM Tris - HCl pH 8.8, 25%(w/v) PEG6000, 50mM olivetolic acid, 5%(v/v) methanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 14, 2014 |
Radiation | Monochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 10098 / % possible obs: 98.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.1 / % possible all: 92.3 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5B08 Resolution: 1.7→32.112 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.58 Å2 / Biso mean: 24.0696 Å2 / Biso min: 11.01 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→32.112 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: 4
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