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Yorodumi- PDB-1cru: SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CAL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cru | ||||||
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Title | SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE FROM ACINETOBACTER CALCOACETICUS IN COMPLEX WITH PQQ AND METHYLHYDRAZINE | ||||||
Components | PROTEIN (SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE / BETA-PROPELLER / SUPERBARREL / COMPLEX WITH THE COFACTOR PQQ AND THE INHIBITOR METHYLHYDRAZINE | ||||||
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: 1.5 Å | ||||||
Authors | Oubrie, A. / Rozeboom, H.J. / Dijkstra, B.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1999 Title: Active-site structure of the soluble quinoprotein glucose dehydrogenase complexed with methylhydrazine: a covalent cofactor-inhibitor complex. Authors: Oubrie, A. / Rozeboom, H.J. / 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. #2: Journal: To be Published Title: Structure and Mechanism of Soluble Quinoprotein Glucose Dehydrogenase Authors: Oubrie, A. / Rozeboom, H.J. / Kalk, K.H. / Olsthoorn, A.J.J. / Duine, J.A. / Dijsktra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cru.cif.gz | 204.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cru.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/1cru ftp://data.pdbj.org/pub/pdb/validation_reports/cr/1cru | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 902 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.3 Å3/Da / Density % sol: 46.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 Method: vapor diffusion / Details: Oubrie, A., (1999) J.Mol.Biol., 289, 319. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-3 / Wavelength: 0.9475 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9475 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. obs: 142076 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / % possible all: 91.2 |
Reflection | *PLUS Num. measured all: 580379 |
Reflection shell | *PLUS % possible obs: 91.2 % |
-Processing
Software |
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Refinement | Resolution: 1.5→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Software | *PLUS Name: 'REFMAC+X-PLOR3.843' / Classification: refinement | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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