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Yorodumi- PDB-1gee: Crystal structure of glucose dehydrogenase mutant Q252L complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gee | ||||||
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Title | Crystal structure of glucose dehydrogenase mutant Q252L complexed with NAD+ | ||||||
Components | GLUCOSE 1-DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / short-chain dehydrogenase/reductase | ||||||
Function / homology | Function and homology information glucose 1-dehydrogenase (NAD+) activity / glucose 1-dehydrogenase (NADP+) activity / glucose 1-dehydrogenase [NAD(P)+] / glucose 1-dehydrogenase [NAD(P)+] activity / sporulation resulting in formation of a cellular spore Similarity search - Function | ||||||
Biological species | Bacillus megaterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. | ||||||
Citation | Journal: To be Published Title: Structural analysis of stability-increasing mutants of glucose dehydrogenase Authors: Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. #1: Journal: J.BIOCHEM.(TOKYO) / Year: 2001 Title: Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution Authors: Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3 Authors: Yamamoto, K. / Kusunoki, M. / Urabe, I. / Tabata, S. / Osaki, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gee.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gee.ent.gz | 173.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gee_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1gee_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1gee_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 1gee_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ge/1gee ftp://data.pdbj.org/pub/pdb/validation_reports/ge/1gee | HTTPS FTP |
-Related structure data
Related structure data | 1g6kC 1gcoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | The biological active form is tetramer. For tetramer1, apply (-x, y, -z)+a to chains A and B. For tetramer2, apply (-x, y, -z)+c to chains E and F. |
-Components
#1: Protein | Mass: 28097.990 Da / Num. of mol.: 4 / Mutation: Q252L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IWG3 / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): KP3998 References: UniProt: P40288, glucose 1-dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-NAD / #3: 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: 1.99 Å3/Da / Density % sol: 37.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium phosphate, PEG2000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 28, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 318004 / % possible obs: 86.5 % / Observed criterion σ(I): 2 / Redundancy: 2.95 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.83 % / Rmerge(I) obs: 0.415 / Num. unique all: 9118 / % possible all: 73.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCO Resolution: 1.6→39.71 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→39.71 Å
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Refine LS restraints |
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