+Open data
-Basic information
Entry | Database: PDB / ID: 5b0c | ||||||
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Title | Polyketide cyclase OAC from Cannabis sativa, Y27F mutant | ||||||
Components | Olivetolic acid cyclase | ||||||
Keywords | LYASE / Cannabis sativa / plant polyketide cyclase | ||||||
Function / homology | Function and homology information 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 | Cannabis sativa (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.602 Å | ||||||
Authors | Yang, X. / Matsui, T. / Mori, T. / Abe, I. / Morita, H. | ||||||
Citation | Journal: Febs J. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b0c.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b0c.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 5b0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b0c_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
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Full document | 5b0c_full_validation.pdf.gz | 432.3 KB | Display | |
Data in XML | 5b0c_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 5b0c_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/5b0c ftp://data.pdbj.org/pub/pdb/validation_reports/b0/5b0c | HTTPS FTP |
-Related structure data
Related structure data | 5b08SC 5b09C 5b0aC 5b0bC 5b0dC 5b0eC 5b0fC 5b0gC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 12214.011 Da / Num. of mol.: 2 / Mutation: Y27F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cannabis sativa (plant) / Gene: OAC / Plasmid: pQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: I6WU39, olivetolic acid cyclase #2: 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: 1.89 Å3/Da / Density % sol: 34.84 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / Details: 100mM Sodium HEPES, pH 7.5, 25%(w/v) PEG3000 |
-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: Nov 22, 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: 1.6→50 Å / Num. obs: 23862 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 42.3 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 13 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.828
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B08 Resolution: 1.602→36.496 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.18 / 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: 50.71 Å2 / Biso mean: 15.6263 Å2 / Biso min: 5.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.602→36.496 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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