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- PDB-1g6k: Crystal structure of glucose dehydrogenase mutant E96A complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g6k | ||||||
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Title | Crystal structure of glucose dehydrogenase mutant E96A complexed with NAD+ | ||||||
![]() | GLUCOSE 1-DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / short-chain dehydrogenase/reductase | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. | ||||||
![]() | ![]() Title: Structural analysis of stability-increasing mutants of glucose dehydrogenase Authors: Yamamoto, K. / Kurisu, G. / Kusunoki, M. / Tabata, S. / Urabe, I. / Osaki, S. #1: ![]() 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: ![]() Title: Crystallization and preliminary X-ray analysis of glucose dehydrogenase from Bacillus megaterium IWG3 Authors: Yamaoto, K. / Kusunoki, M. / Urabe, I. / Tabata, S. / Osaki, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.8 KB | Display | ![]() |
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PDB format | ![]() | 170.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 42.6 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1geeC ![]() 1gcoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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. |
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Components
#1: Protein | Mass: 28054.924 Da / Num. of mol.: 4 / Mutation: E96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG2000, sodium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. obs: 294512 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 4.78 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.208 / Num. unique all: 5172 / % possible all: 80.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GCO Resolution: 2→39.95 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→39.95 Å
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Refine LS restraints |
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