+Open data
-Basic information
Entry | Database: PDB / ID: 7d3a | ||||||
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Title | flavone reductase | ||||||
Components | Cd1 | ||||||
Keywords | FLAVOPROTEIN / flavone reductase / FMN / apigenin | ||||||
Function / homology | NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavoprotein-like superfamily / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / Chem-AGI / FLAVIN MONONUCLEOTIDE / FMN reductase / Flavin reductase Function and homology information | ||||||
Biological species | Flavonifractor plautii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.552 Å | ||||||
Authors | Hong, S. / Yang, G.H. / Zhang, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria. Authors: Yang, G. / Hong, S. / Yang, P. / Sun, Y. / Wang, Y. / Zhang, P. / Jiang, W. / Gu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d3a.cif.gz | 125.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d3a.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 7d3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/7d3a ftp://data.pdbj.org/pub/pdb/validation_reports/d3/7d3a | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34433.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) Flavonifractor plautii (bacteria) / Gene: A4U99_05915, ERS852544_00852, GXM20_05520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174NXS8, UniProt: G9YLX2*PLUS |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-AGI / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M magnesium formate dihydrate and 15 w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 22019 / % possible obs: 99.9 % / Redundancy: 23.1 % / CC1/2: 0.887 / Net I/σ(I): 28.67 |
Reflection shell | Resolution: 2.59→2.64 Å / Num. unique obs: 12318 / CC1/2: 0.887 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.552→28.618 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.39 / Stereochemistry target values: ML
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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 max: 110.48 Å2 / Biso mean: 38.3258 Å2 / Biso min: 10.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.552→28.618 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 31.3098 Å / Origin y: -18.0378 Å / Origin z: -1.7779 Å
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Refinement TLS group |
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