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Yorodumi- PDB-3aut: Crystal structure of Bacillus megaterium glucose dehydrogenase 4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aut | ||||||
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Title | Crystal structure of Bacillus megaterium glucose dehydrogenase 4 in complex with NADH | ||||||
Components | Glucose 1-dehydrogenase 4 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / NAD / Oxidation-reduction process / Cytosol | ||||||
Function / homology | Function and homology information glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / identical protein binding Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Nishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, T. | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Structure-guided mutagenesis for the improvement of substrate specificity of Bacillus megaterium glucose 1-dehydrogenase IV Authors: Nishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aut.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aut.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 3aut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3aut_validation.pdf.gz | 760.6 KB | Display | wwPDB validaton report |
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Full document | 3aut_full_validation.pdf.gz | 765.5 KB | Display | |
Data in XML | 3aut_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 3aut_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/3aut ftp://data.pdbj.org/pub/pdb/validation_reports/au/3aut | HTTPS FTP |
-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: 29199.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IAM 1030 / Gene: gdhIV / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: P39485, glucose 1-dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-NAI / | #3: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 43.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate pH 6.5, 0.2M magnesium chloride, 50% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 12, 2010 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 32754 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.81 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.94 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.96 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.382 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 35.374 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Total num. of bins used: 20
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