+Open data
-Basic information
Entry | Database: PDB / ID: 8v8m | |||||||||
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Title | Switchgrass Chalcone Synthase | |||||||||
Components | Chalcone synthase | |||||||||
Keywords | TRANSFERASE / Chalcone Synthase / Flavonoids / Chalcones | |||||||||
Function / homology | Function and homology information chalcone synthase / flavonoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | |||||||||
Biological species | Panicum virgatum (switchgrass) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 | 8v8m.cif.gz | 323.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v8m.ent.gz | 258.4 KB | Display | PDB format |
PDBx/mmJSON format | 8v8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v8m_validation.pdf.gz | 1011.7 KB | Display | wwPDB validaton report |
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Full document | 8v8m_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8v8m_validation.xml.gz | 64.2 KB | Display | |
Data in CIF | 8v8m_validation.cif.gz | 92.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/8v8m ftp://data.pdbj.org/pub/pdb/validation_reports/v8/8v8m | HTTPS FTP |
-Related structure data
Related structure data | 8v8lC 8v8nC 8v8oC 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: 43348.637 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Panicum virgatum (switchgrass) / Gene: PVAP13_8KG261900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8T0PQ54 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Formate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→48.72 Å / Num. obs: 233811 / % possible obs: 93.37 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.1447 / Net I/σ(I): 4.43 |
Reflection shell | Resolution: 1.82→1.885 Å / Rmerge(I) obs: 0.6048 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 21963 / % possible all: 91.22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→48.72 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.35 / 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: 1.82→48.72 Å
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Refine LS restraints |
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LS refinement shell |
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