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Yorodumi- PDB-1cq1: Soluble Quinoprotein Glucose Dehydrogenase from Acinetobacter Cal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cq1 | ||||||
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Title | Soluble Quinoprotein Glucose Dehydrogenase from Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose | ||||||
Components | SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / BETA-PROPELLER / SUPERBARREL / COMPLEX WITH COFACTOR AND SUBSTRATE | ||||||
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 / Resolution: 1.9 Å | ||||||
Authors | Oubrie, A. / Rozeboom, H.J. / Dijkstra, B.W. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Structure and mechanism of soluble quinoprotein glucose dehydrogenase. Authors: Oubrie, A. / Rozeboom, H.J. / Kalk, K.H. / Olsthoorn, A.J. / Duine, J.A. / Dijkstra, B.W. #1: Journal: J.Mol.Biol. / Year: 1999 Title: The 1.7 Angstrom crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal sequence repeat Authors: Oubrie, A. / Rozeboom, H.J. / Kalk, K.H. / Duine, J.A. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cq1.cif.gz | 195 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cq1.ent.gz | 158.1 KB | Display | PDB format |
PDBx/mmJSON format | 1cq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cq1_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1cq1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1cq1_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 1cq1_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/1cq1 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/1cq1 | 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: 50293.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Cellular location: PERIPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P13650, EC: 1.1.99.17 #2: Sugar | #3: Chemical | ChemComp-CA / #4: Chemical | #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: 2.31 Å3/Da / Density % sol: 46.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: PEG 6000, SODIUM CHLORIDE, CALCIUM CHLORIDE, TRIS, GLYCINE, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0736 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0736 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 92216 / Num. obs: 92032 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.814 / % possible all: 98.1 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: 'REFMAC, X-PLOR 3.843' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 3 |