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- PDB-8dqq: Crystal structure of Arabidopsis thaliana COSY in complex with sc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dqq | ||||||||||||
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Title | Crystal structure of Arabidopsis thaliana COSY in complex with scopoletin | ||||||||||||
![]() | Coumarin Synthase | ||||||||||||
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Function / homology | coumarin biosynthetic process / ![]() ![]() ![]() ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, C.Y. / Mitchell, A.J. / Gutierrez, M. / Weng, J.K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Emergence of a proton exchange-based isomerization and lactonization mechanism in the plant coumarin synthase COSY. Authors: Kim, C.Y. / Mitchell, A.J. / Kastner, D.W. / Albright, C.E. / Gutierrez, M.A. / Glinkerman, C.M. / Kulik, H.J. / Weng, J.K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 221.5 KB | Display | ![]() |
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PDB format | ![]() | 142.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dqoSC ![]() 8dqpC ![]() 8dqrC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 49732.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-07L / | ![]() #3: Chemical | #4: Chemical | ChemComp-ACT / | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.45 % |
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Crystal grow![]() | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 50 mM calcium acetate, 0.1 M sodium cacodylate pH 6.5, 20% glycerol, 500 uM umbelliferone, 5 mg/mL protein PH range: 6.5-7.5 / Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.33→136.81 Å / Num. obs: 40091 / % possible obs: 97.43 % / Redundancy: 1.9 % / Biso Wilson estimate: 48.47 Å2 / CC1/2: 0.991 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.33→2.413 Å / Rmerge(I) obs: 0.7117 / Mean I/σ(I) obs: 1 / Num. unique obs: 7339 / CC1/2: 0.441 / CC star: 0.782 / Rpim(I) all: 0.7117 / Rrim(I) all: 1 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 8DQO Resolution: 2.33→136.81 Å / SU ML: 0.3272 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.8537 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 58.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→136.81 Å
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Refine LS restraints |
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LS refinement shell |
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