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Yorodumi- PDB-7yj5: Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yj5 | ||||||||||||
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Title | Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) | ||||||||||||
Components | Stenoloma chusanum chalcone synthase 1 (ScCHS1) | ||||||||||||
Keywords | TRANSFERASE / flavonoids biosynthesis / chalcone synthase / Stenoloma chusanum | ||||||||||||
Function / homology | trimethylamine oxide Function and homology information | ||||||||||||
Biological species | Odontosoria chusana (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å | ||||||||||||
Authors | Li, J.X. / Cheng, A.X. / Zhang, P. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J Integr Plant Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yj5.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yj5.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 7yj5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yj5_validation.pdf.gz | 729.7 KB | Display | wwPDB validaton report |
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Full document | 7yj5_full_validation.pdf.gz | 733.3 KB | Display | |
Data in XML | 7yj5_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 7yj5_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/7yj5 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/7yj5 | HTTPS FTP |
-Related structure data
Related structure data | 7yj6C 7yj7C 7yj8C 7yj9C 7yjaC 7yjbC 7veyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Odontosoria chusana (plant) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-TMO / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris-HCl pH 8.5, 20% (w/v) PEG MME 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 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: 1.7→41.789 Å / Num. obs: 40032 / % possible obs: 91.59 % / Redundancy: 12.2 % / CC1/2: 0.994 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.701→1.762 Å / Num. unique obs: 2862 / CC1/2: 0.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VEY Resolution: 1.701→41.789 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.94 / 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: 89.38 Å2 / Biso mean: 19.311 Å2 / Biso min: 2.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.701→41.789 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: 49.2725 Å / Origin y: 48.0313 Å / Origin z: 30.9128 Å
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Refinement TLS group |
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