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Yorodumi- PDB-8rg1: Soluble glucose dehydrogenase from acinetobacter calcoaceticus - ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rg1 | ||||||
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Title | Soluble glucose dehydrogenase from acinetobacter calcoaceticus - wild type pH8 | ||||||
Components | Quinoprotein glucose dehydrogenase B | ||||||
Keywords | OXIDOREDUCTASE / Wild type / PQQ | ||||||
Function / homology | Function and homology information glucose 1-dehydrogenase (PQQ, quinone) / quinoprotein glucose dehydrogenase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Acinetobacter calcoaceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||
Authors | Lublin, V. / Chavas, L. / Stines-Chaumeil, C. / Kauffmann, B. / Giraud, M.F. / Thompson, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Biosci.Rep. / Year: 2024 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. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rg1.cif.gz | 623.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rg1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/8rg1 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/8rg1 | HTTPS FTP |
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-Related structure data
Related structure data | 8re0C 8rfkC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50293.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: gdhB / Production host: Escherichia coli (E. coli) / References: UniProt: P13650 #2: Chemical | Mass: 364.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8N2O10 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.27 Å3/Da / Density % sol: 45.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, 100 mM TRIS pH8, 2 mM ZnCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. obs: 199471 / % possible obs: 98.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.19→1.233 Å / Redundancy: 2 % / Rmerge(I) obs: 0.42 / Num. unique obs: 1815 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.42 / Rrim(I) all: 0.59 / % possible all: 6.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→42.56 Å / SU ML: 0.109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.971 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→42.56 Å
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Refine LS restraints |
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LS refinement shell |
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