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- PDB-7cbf: Crystal structure of benzophenone synthase from Garcinia mangosta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cbf | ||||||
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Title | Crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis | ||||||
![]() | 2,4,6-trihydroxybenzophenone synthase | ||||||
![]() | TRANSFERASE / ACYLTRANSFERASE / BENZOPHENONE SYNTHASE / POLYKETIDE SYNTHASE / GmBPS | ||||||
Function / homology | ![]() 2,4,6-trihydroxybenzophenone synthase / tetrahydroxybenzophenone synthase activity / trihydroxybenzophenone synthase activity / benzoyl-CoA metabolic process / malonyl-CoA metabolic process / biosynthetic process / acyltransferase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Songsiriritthigul, C. / Nualkaew, N. / Chen, C.-J. | ||||||
![]() | ![]() Title: Crystal structure of benzophenone synthase from Garcinia mangostana L. pericarps reveals basis for substrate specificity and catalysis. Authors: Songsiriritthigul, C. / Nualkaew, N. / Ketudat-Cairnsb, J. / Chen, C.-J. #1: ![]() Title: Benzophenone synthase from Garcinia mangostana L. pericarps Authors: Nualkaew, N. / Morita, H. / Shimokawa, Y. / Kinjo, K. / Kushiro, T. / De-Eknamkul, W. / Ebizuka, Y. / Abe, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.2 KB | Display | ![]() |
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PDB format | ![]() | 127.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466.7 KB | Display | ![]() |
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Full document | ![]() | 473.3 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cgkS 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: 44045.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: L7NCQ3, 2,4,6-trihydroxybenzophenone synthase #2: Chemical | #3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % / Description: rectangular morphology |
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Crystal grow | Temperature: 291 K / Method: batch mode / pH: 6.2 / Details: 20% (w/v) PEG 3,350, 0.2 M ammonium iodide, pH 6.2 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2015 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 35272 / % possible obs: 99.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.52 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 9.67 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.14 / Num. unique obs: 6660 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CGK Resolution: 2.301→24.347 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.648 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.218 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.241 Å2
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Refinement step | Cycle: LAST / Resolution: 2.301→24.347 Å
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Refine LS restraints |
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LS refinement shell |
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