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Yorodumi- PDB-7bq6: Crystal structure of Pennisetum glaucum monodehydroascorbate reductase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bq6 | ||||||
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Title | Crystal structure of Pennisetum glaucum monodehydroascorbate reductase | ||||||
Components | Pg protein | ||||||
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: 1.89 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 | 7bq6.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bq6.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 7bq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/7bq6 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/7bq6 | HTTPS FTP |
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-Related structure data
Related structure data | 7bviC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46843.133 Da / Num. of mol.: 1 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) |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-TRS / |
#4: Chemical | ChemComp-ACT / |
#5: 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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M Ammonium acetate 0.1 M Sodium citrate tribasic dihydrate 5.6 30 %w/v Polyethylene glycol 4,000 PH range: 5.6 - 6.4 |
-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: 1.89→61.44 Å / Num. obs: 36259 / % possible obs: 99 % / Redundancy: 5.4 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.132 / Net I/av σ(I): 2.09 / Net I/σ(I): 2.09 |
Reflection shell | Resolution: 1.894→1.926 Å / Num. unique obs: 1804 / CC1/2: 0.707 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5jci Resolution: 1.89→61.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.127
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Displacement parameters | Biso max: 102.51 Å2 / Biso mean: 25.02 Å2 / Biso min: 10.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.89→61.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 6.4113 Å / Origin y: 18.9507 Å / Origin z: 151.933 Å
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Refinement TLS group | Selection details: { A|* } |