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Yorodumi- PDB-7bvi: Crystal structure of Pennisetum glaucum monodehydroascorbate reductase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bvi | ||||||
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Title | Crystal structure of Pennisetum glaucum monodehydroascorbate reductase | ||||||
Components | Pennisetum glaucum monodehydroascorbate reductase | ||||||
Keywords | OXIDOREDUCTASE / Nucleotide Binding / Oxidoreductase Activity / Monodehydroascorbate Reductase (nadh) Activity / Flavin Adenine Dinucleotide Binding | ||||||
Function / homology | ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Cenchrus americanus (bulrush millet) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.391 Å | ||||||
Authors | Sonkar, K.S. / Arulandu, A. / Achary, M.M. / Reddy, M.K. | ||||||
Funding support | India, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Biochemical and structural characterization of a robust and thermostable ascorbate recycling monodehydroascorbate reductase (MDHAR) from stress adapted pearl millet. Authors: Sonkar, K.S. / Achary, V.M.M. / Sahoo, S. / Reddy, M.K. / Arockiasamy, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bvi.cif.gz | 349.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bvi.ent.gz | 279.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bvi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/7bvi ftp://data.pdbj.org/pub/pdb/validation_reports/bv/7bvi | HTTPS FTP |
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-Related structure data
Related structure data | 7bq6C 5jciS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 46843.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cenchrus americanus (bulrush millet) / Gene: MDHAR / Plasmid: pETM30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: monodehydroascorbate reductase (NADH) #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-ACT / #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: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M) Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate pH 6.5 30% w/v Polyethylene glycol 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 27, 2018 / Details: insertion device (ID) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.391→72.34 Å / Num. obs: 61346 / % possible obs: 92.17 % / Redundancy: 3.9 % / Biso Wilson estimate: 37.89 Å2 / CC1/2: 0.993 / Net I/σ(I): 2.17 |
Reflection shell | Resolution: 2.391→2.432 Å / Num. unique obs: 237394 / CC1/2: 0.993 / Rrim(I) all: 0.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5jci Resolution: 2.391→72.34 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 0.641 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.619 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.266
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Displacement parameters | Biso max: 64.26 Å2 / Biso mean: 26.31 Å2 / Biso min: 6.45 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.391→72.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.391→2.41 Å / Rfactor Rfree error: 0
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