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- PDB-8rfk: Soluble glucose dehydrogenase from acinetobacter calcoaceticus - ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rfk | ||||||
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Title | Soluble glucose dehydrogenase from acinetobacter calcoaceticus - single mutant pH8 | ||||||
![]() | Quinoprotein glucose dehydrogenase B | ||||||
![]() | OXIDOREDUCTASE / Double point mutation | ||||||
Function / homology | ![]() glucose 1-dehydrogenase (PQQ, quinone) / quinoprotein glucose dehydrogenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lublin, V. / Chavas, L. / Stines-Chaumeil, C. / Kauffmann, B. / Giraud, M.F. / Thompson, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Does Acinetobacter calcoaceticus glucose dehydrogenase produce self-damaging H2O2? Authors: Lublin, V. / Kauffmann, B. / Engilberge, S. / Durola, F. / Gounel, S. / Bichon, S. / Jean, C. / Mano, N. / Giraud, M.F. / Chavas, L.M.G.H. / Thureau, A. / Thompson, A. / Stines-Chaumeil, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 458 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 45.8 KB | Display | |
Data in CIF | ![]() | 72.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8re0C ![]() 8rg1C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50277.207 Da / Num. of mol.: 2 / Mutation: D143E,Y343F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | Mass: 364.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8N2O10 / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, TRIS, Lithium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→46.5 Å / Num. obs: 131392 / % possible obs: 97.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.41 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.132 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.54→1.63 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.58 / Num. unique obs: 18670 / CC1/2: 0.36 / Rrim(I) all: 1.59 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.56→42.73 Å
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Refine LS restraints |
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LS refinement shell |
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