[English] 日本語
Yorodumi- PDB-7yj9: Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yj9 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Stenoloma chusanum chalcone synthase 1 (ScCHS1) complex with CoA and Naringenin | ||||||||||||
Components | chalcone synthase 1 (ScCHS1) | ||||||||||||
Keywords | TRANSFERASE / flavonoids biosynthesis / chalcone synthase / Stenoloma chusanum | ||||||||||||
Function / homology | COENZYME A / NARINGENIN Function and homology information | ||||||||||||
Biological species | Odontosoria chusana (plant) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å | ||||||||||||
Authors | Li, J.X. / Cheng, A.X. / Zhang, P. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7yj9.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7yj9.ent.gz | 140.1 KB | Display | PDB format |
PDBx/mmJSON format | 7yj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/7yj9 ftp://data.pdbj.org/pub/pdb/validation_reports/yj/7yj9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7yj5C 7yj6C 7yj7C 7yj8C 7yjaC 7yjbC 7veyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-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) |
---|---|
#2: Chemical | ChemComp-NAR / |
#3: Chemical | ChemComp-COA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % |
---|---|
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 |
---|---|
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: 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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -16.0415 Å / Origin y: -11.9315 Å / Origin z: 10.3401 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|