+Open data
-Basic information
Entry | Database: PDB / ID: 8few | |||||||||
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Title | Flavanone 4-Reductase from Sorghum bicolor-naringenin complex | |||||||||
Components | 3-deoxyanthocyanidin synthase | |||||||||
Keywords | OXIDOREDUCTASE / SDR type protein / flavanone / sorghum | |||||||||
Function / homology | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / nucleotide binding / NARINGENIN / 3-deoxyanthocyanidin synthase Function and homology information | |||||||||
Biological species | Sorghum bicolor (sorghum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | |||||||||
Authors | Zhang, B. / Kang, C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Similarities and Overlapping Activities among Dihydroflavonol 4-Reductase, Flavanone 4-Reductase, and Anthocyanidin Reductase Offer Metabolic Flexibility in the Flavonoid Pathway. Authors: Lewis, J.A. / Zhang, B. / Harza, R. / Palmer, N. / Sarath, G. / Sattler, S.E. / Twigg, P. / Vermerris, W. / Kang, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8few.cif.gz | 151.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8few.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 8few.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/8few ftp://data.pdbj.org/pub/pdb/validation_reports/fe/8few | HTTPS FTP |
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-Related structure data
Related structure data | 8femC 8fenC 8fetC 8feuC 8fevC 8fioC 8fipC 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
#1: Protein | Mass: 37843.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Production host: Escherichia coli (E. coli) / References: UniProt: C5YGL7 #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 4.7 Å3/Da / Density % sol: 73.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES, pH 7.5, 2 M Ammonium Sulfate and 2 % PEG 400 |
-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: 0.9765 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→47.61 Å / Num. obs: 93749 / % possible obs: 99.88 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 20.32 |
Reflection shell | Resolution: 2.02→2.092 Å / Num. unique obs: 9256 / CC1/2: 0.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→47.61 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.26 / 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: 2.02→47.61 Å
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Refine LS restraints |
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LS refinement shell |
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