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- PDB-7yj9: Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yj9 | ||||||||||||
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Title | Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with CoA and Naringenin | ||||||||||||
![]() | chalcone synthase 1 (ScCHS1) | ||||||||||||
![]() | TRANSFERASE / flavonoids biosynthesis / chalcone synthase / Stenoloma chusanum | ||||||||||||
Function / homology | COENZYME A / NARINGENIN![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, J.X. / Cheng, A.X. / Zhang, P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular and structural characterization of a promiscuous chalcone synthase from the fern species Stenoloma chusanum. Authors: Ni, R. / Niu, M. / Fu, J. / Tan, H. / Zhu, T.T. / Zhang, J. / Lou, H.X. / Zhang, P. / Li, J.X. / Cheng, A.X. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.6 KB | Display | ![]() |
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PDB format | ![]() | 140.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yj5C ![]() 7yj6C ![]() 7yj7C ![]() 7yj8C ![]() 7yjaC ![]() 7yjbC ![]() 7veyS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 44506.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NAR / |
#3: Chemical | ChemComp-COA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Sodium chloride, 0.1 M HEPES pH 7.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.851→36.197 Å / Num. obs: 31014 / % possible obs: 89.78 % / Redundancy: 12.1 % / CC1/2: 0.997 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.851→1.917 Å / Num. unique obs: 2018 / CC1/2: 0.687 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VEY Resolution: 1.851→36.197 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.57 / 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: 82.48 Å2 / Biso mean: 25.6579 Å2 / Biso min: 8.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.851→36.197 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -16.0415 Å / Origin y: -11.9315 Å / Origin z: 10.3401 Å
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Refinement TLS group |
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