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Yorodumi- PDB-7yj8: Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yj8 | ||||||||||||
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Title | Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with Pinocembrin | ||||||||||||
Components | chalcone synthase 1 (ScCHS1) | ||||||||||||
Keywords | TRANSFERASE / flavonoids biosynthesis / chalcone synthase / Stenoloma chusanum | ||||||||||||
Function / homology | pinocembrin Function and homology information | ||||||||||||
Biological species | Odontosoria chusana (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 7yj8.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yj8.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yj8_validation.pdf.gz | 725 KB | Display | wwPDB validaton report |
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Full document | 7yj8_full_validation.pdf.gz | 734.1 KB | Display | |
Data in XML | 7yj8_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7yj8_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/7yj8 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/7yj8 | HTTPS FTP |
-Related structure data
Related structure data | 7yj5C 7yj6C 7yj7C 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-KML / |
#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: 2.3 Å3/Da / Density % sol: 46.59 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
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: 2.2→27.395 Å / Num. obs: 26056 / % possible obs: 86.27 % / Redundancy: 12.1 % / CC1/2: 0.996 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 2.2→2.279 Å / Num. unique obs: 1315 / CC1/2: 0.986 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7VEY Resolution: 2.2→27.395 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.83 / 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: 109.48 Å2 / Biso mean: 43.8759 Å2 / Biso min: 12.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→27.395 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: -17.3509 Å / Origin y: -24.6019 Å / Origin z: 10.3941 Å
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Refinement TLS group |
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