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Open data
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Basic information
Entry | Database: PDB / ID: 5b0a | ||||||
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Title | Polyketide cyclase OAC from Cannabis sativa, H5Q mutant | ||||||
![]() | 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 | ![]() | 54.2 KB | Display | ![]() |
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PDB format | ![]() | 37.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.8 KB | Display | ![]() |
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Full document | ![]() | 435.3 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b08SC ![]() 5b09C ![]() 5b0bC ![]() 5b0cC ![]() 5b0dC ![]() 5b0eC ![]() 5b0fC ![]() 5b0gC 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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Unit cell |
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Components
#1: Protein | Mass: 12219.993 Da / Num. of mol.: 2 / Mutation: H5Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.97 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop Details: 100mM Sodium acetate, 25%(w/v) PEG4000, 8%(v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 10898 / % possible obs: 95.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.024 / Net I/σ(I): 31.9 |
Reflection shell | Resolution: 2.1→2.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 13 / % possible all: 91.2 |
-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: 2.1→34.654 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.49 / 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: 73.31 Å2 / Biso mean: 27.8493 Å2 / Biso min: 13.02 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→34.654 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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