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Yorodumi- PDB-8fio: Hypothetical anthocyanidin reductase from Sorghum bicolor-NADP(H)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fio | |||||||||
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Title | Hypothetical anthocyanidin reductase from Sorghum bicolor-NADP(H) and naringenin complex | |||||||||
Components | Epimerase domain-containing protein | |||||||||
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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NARINGENIN / NAD-dependent epimerase/dehydratase domain-containing protein Function and homology information | |||||||||
Biological species | Sorghum bicolor (sorghum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 | 8fio.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fio.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 8fio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fio_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8fio_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8fio_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 8fio_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/8fio ftp://data.pdbj.org/pub/pdb/validation_reports/fi/8fio | HTTPS FTP |
-Related structure data
Related structure data | 8femC 8fenC 8fetC 8feuC 8fevC 8fewC 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: 37639.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3006G226700 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B6PND3 #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: 2.69 Å3/Da / Density % sol: 54.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 sodium chloride, 0.1 M, HEPES, pH 7.5, 1.6 M ammonium sulfate |
-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: 0.9774 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 12, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→42.58 Å / Num. obs: 55230 / % possible obs: 93.84 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.0888 / Net I/σ(I): 8.25 |
Reflection shell | Resolution: 1.97→2.04 Å / Num. unique obs: 3590 / CC1/2: 0.327 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→42.58 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.85 / 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: 1.97→42.58 Å
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Refine LS restraints |
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LS refinement shell |
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