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Yorodumi- PDB-8dlc: Crystal structure of chalcone-isomerase like protein from Vitis v... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dlc | ||||||
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Title | Crystal structure of chalcone-isomerase like protein from Vitis vinifera (VvCHIL) | ||||||
Components | Chalcone-flavonone isomerase family protein | ||||||
Keywords | SIGNALING PROTEIN / Chalcone isomerase-fold | ||||||
Function / homology | Chalcone--flavonone isomerase 3-like / intramolecular lyase activity / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase / Chalcone isomerase superfamily / Chalcone-flavonone isomerase family protein Function and homology information | ||||||
Biological species | Vitis vinifera (wine grape) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wolf Saxon, E. / Moorman, C. / Castro, A. / Ruiz, A. / Mallari, J.P. / Burke, J.R. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Regulatory ligand binding in plant chalcone isomerase-like (CHIL) proteins. Authors: Wolf-Saxon, E.R. / Moorman, C.C. / Castro, A. / Ruiz-Rivera, A. / Mallari, J.P. / Burke, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dlc.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dlc.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dlc_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 8dlc_full_validation.pdf.gz | 421.4 KB | Display | |
Data in XML | 8dlc_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 8dlc_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dl/8dlc ftp://data.pdbj.org/pub/pdb/validation_reports/dl/8dlc | HTTPS FTP |
-Related structure data
Related structure data | 8dldC 4dokS 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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Details | The dimer observed crystallographically has not been proven to represent the true biological inter-subunit interaction; however, it has been shown that the protein is dimeric. |
-Components
#1: Protein | Mass: 24041.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: CHI3_0, CK203_016634 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A438J2L0 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.85 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350 and 200 mM potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→42.8 Å / Num. obs: 19994 / % possible obs: 100 % / Redundancy: 15.8 % / Biso Wilson estimate: 22.51 Å2 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.05 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2818 / Rpim(I) all: 0.439 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4dok Resolution: 1.9→42.8 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.9878 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: 27.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→42.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.9152614717 Å / Origin y: -13.7142768208 Å / Origin z: 12.5134712215 Å
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Refinement TLS group | Selection details: all |