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Yorodumi- PDB-4ynt: Crystal structure of Aspergillus flavus FAD glucose dehydrogenase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ynt | ||||||
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Title | Crystal structure of Aspergillus flavus FAD glucose dehydrogenase | ||||||
Components | Glucose oxidase, putative | ||||||
Keywords | OXIDOREDUCTASE / Glucose dehydrogenase / FAD | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Aspergillus flavus NRRL3357 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Yoshida, H. / Sakai, G. / Kojima, K. / Kamitori, S. / Sode, K. | ||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Structural analysis of fungus-derived FAD glucose dehydrogenase Authors: Yoshida, H. / Sakai, G. / Mori, K. / Kojima, K. / Kamitori, S. / Sode, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ynt.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ynt.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ynt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/4ynt ftp://data.pdbj.org/pub/pdb/validation_reports/yn/4ynt | HTTPS FTP |
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-Related structure data
Related structure data | 4ynuC 1cf3S C: citing same article (ref.) S: Starting model for refinement |
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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: 61548.922 Da / Num. of mol.: 1 / Fragment: UNP residues 24-593 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus flavus NRRL3357 (mold) / Strain: NRRL 3357 / Gene: AFLA_076820 / Plasmid: pET30c / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: B8MX95, EC: 1.1.5.9 |
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#2: Chemical | ChemComp-FDA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BisTris, 20-25 % PEG 3350 / PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.77→50 Å / Num. obs: 45130 / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.071 / Χ2: 1.381 / Net I/av σ(I): 17.424 / Net I/σ(I): 15.2 / Num. measured all: 143309 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CF3 Resolution: 1.78→48.75 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.602 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.45 Å2 / Biso mean: 23.958 Å2 / Biso min: 11.82 Å2
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Refinement step | Cycle: final / Resolution: 1.78→48.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.775→1.821 Å / Total num. of bins used: 20
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