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Yorodumi- PDB-1rwb: Cooperative Effect of Two Surface Amino Acid Mutations (Q252L and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rwb | ||||||
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Title | Cooperative Effect of Two Surface Amino Acid Mutations (Q252L and E170K) of Glucose Dehydrogenase from Bacillus megaterium IWG3 for the stabilization of Oligomeric State | ||||||
Components | Glucose 1-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 / Rigid Body / Resolution: 2 Å | ||||||
Authors | Baik, S.-H. / Michel, F. / Haser, R. / Harayama, S. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2005 Title: Cooperative effect of two surface amino acid mutations (Q252L and E170K) in glucose dehydrogenase from Bacillus megaterium IWG3 on stabilization of its oligomeric state. Authors: Baik, S.H. / Michel, F. / Aghajari, N. / Haser, R. / Harayama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rwb.cif.gz | 216.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rwb.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwb ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwb | HTTPS FTP |
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-Related structure data
Related structure data | 1gcoS S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 28098.057 Da / Num. of mol.: 4 / Mutation: Q252L, E170K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: IWG3 / Production host: Escherichia coli (E. coli) 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: 2.03 Å3/Da / Density % sol: 39.47 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 6000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.3 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
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: BM30A / Wavelength: 0.95 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 5, 2002 |
Radiation | Monochromator: two crystal monochromator between two cylindrical parabolic mirrors Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→40 Å / Num. obs: 78937 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.06 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.83→1.92 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2274 / Rsym value: 0.19 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Num. obs: 61998 / Redundancy: 3.1 % / Num. measured all: 193166 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 5.9 |
-Processing
Software |
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Refinement | Method to determine structure: Rigid Body Starting model: PDB Entry 1GCO Resolution: 2→14.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2792389.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.2644 Å2 / ksol: 0.356288 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 15 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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