+Open data
-Basic information
Entry | Database: PDB / ID: 8v8o | |||||||||
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Title | Switchgrass Chalcone Isomerase-Like Protein | |||||||||
Components | Chalcone-flavonone isomerase family protein | |||||||||
Keywords | PROTEIN BINDING / Chalcone Synthase / Flavonoids / TRANSFERASE | |||||||||
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 | Panicum virgatum (switchgrass) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | |||||||||
Authors | Lewis, J.A. / Kang, C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Int J Mol Sci / Year: 2024 Title: Structural and Interactional Analysis of the Flavonoid Pathway Proteins: Chalcone Synthase, Chalcone Isomerase and Chalcone Isomerase-like Protein. Authors: Lewis, J.A. / Jacobo, E.P. / Palmer, N. / Vermerris, W. / Sattler, S.E. / Brozik, J.A. / Sarath, G. / Kang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v8o.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v8o.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 8v8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v8o_validation.pdf.gz | 248.7 KB | Display | wwPDB validaton report |
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Full document | 8v8o_full_validation.pdf.gz | 248.6 KB | Display | |
Data in XML | 8v8o_validation.xml.gz | 921 B | Display | |
Data in CIF | 8v8o_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/8v8o ftp://data.pdbj.org/pub/pdb/validation_reports/v8/8v8o | HTTPS FTP |
-Related structure data
Related structure data | 8v8lC 8v8mC 8v8nC 8v8pC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24283.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_8KG022400 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0PCS1 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 1.1 M Ammonium Tartrate Dibasic pH=7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2023 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 12646 / % possible obs: 99.7 % / Redundancy: 12.4 % / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.108 / Rrim(I) all: 0.387 / Χ2: 0.549 / Net I/σ(I): 1.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→45.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.21→45.54 Å
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Refine LS restraints |
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LS refinement shell |
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