+Open data
-Basic information
Entry | Database: PDB / ID: 3wic | ||||||
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Title | Structure of a substrate/cofactor-unbound glucose dehydrogenase | ||||||
Components | Glucose 1-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | ||||||
Function / homology | Function and homology information non-phosphorylated glucose catabolic process / glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / D-glucose binding / NADP+ binding / NAD+ binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Thermoplasma volcanium (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Sakuraba, H. / Kanoh, Y. / Yoneda, K. / Ohshima, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural insight into glucose dehydrogenase from the thermoacidophilic archaeon Thermoplasma volcanium. Authors: Kanoh, Y. / Uehara, S. / Iwata, H. / Yoneda, K. / Ohshima, T. / Sakuraba, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wic.cif.gz | 292.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wic.ent.gz | 237 KB | Display | PDB format |
PDBx/mmJSON format | 3wic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wic_validation.pdf.gz | 487.1 KB | Display | wwPDB validaton report |
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Full document | 3wic_full_validation.pdf.gz | 519.8 KB | Display | |
Data in XML | 3wic_validation.xml.gz | 56.9 KB | Display | |
Data in CIF | 3wic_validation.cif.gz | 76.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3wic ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3wic | HTTPS FTP |
-Related structure data
Related structure data | 3widC 3wieC 2cd9S 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: 40296.902 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma volcanium (archaea) Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1 Gene: gdh, TV1048, TVG1073292 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q979W2, glucose 1-dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PGO / #4: Chemical | ChemComp-1PE / #5: 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: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 400, 1,2-propanediol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 9, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 48068 / Num. obs: 48068 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2cd9 Resolution: 2.6→49.08 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.885 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.344 / 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: 111.78 Å2 / Biso mean: 35.868 Å2 / Biso min: 10.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→49.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.665 Å / Total num. of bins used: 20
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