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Yorodumi- PDB-2exi: Structure of the family43 beta-Xylosidase D15G mutant from geobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2exi | ||||||
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Title | Structure of the family43 beta-Xylosidase D15G mutant from geobacillus stearothermophilus | ||||||
Components | beta-D-xylosidase | ||||||
Keywords | HYDROLASE / glykosidase / hydrolsase / xylosidase / family43 | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Brux, C. / Niefind, K. / Shallom-Shezifi, D. / Shoham, Y. / Schomburg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The Structure of an Inverting GH43 beta-Xylosidase from Geobacillus stearothermophilus with its Substrate Reveals the Role of the Three Catalytic Residues. Authors: Brux, C. / Ben-David, A. / Shallom-Shezifi, D. / Leon, M. / Niefind, K. / Shoham, G. / Shoham, Y. / Schomburg, D. #1: Journal: To be Published Title: Crystallization and preliminary crystallographic analysis of a family 43 ?-D-xylosidase from Geobacillus stearothermophilus T-6 #2: Journal: Biochemistry / Year: 2005 Title: Biochemical Characterization and Identification of the Catalytic Residues of a Family 43 beta-D-Xylosidase from Geobacillus stearothermophilus T-6 | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2exi.cif.gz | 484.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2exi.ent.gz | 392.6 KB | Display | PDB format |
PDBx/mmJSON format | 2exi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2exi ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2exi | HTTPS FTP |
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-Related 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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Details | The biological assembly is a tetramer |
-Components
#1: Protein | Mass: 61927.258 Da / Num. of mol.: 4 / Mutation: D15G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pET9d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q68HB3, UniProt: Q09LX0*PLUS, xylan 1,4-beta-xylosidase #2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-GOL / #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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 17% PEG 6000, 0.1M MES, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9239 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 2005 |
Radiation | Monochromator: Bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9239 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 126702 / Num. obs: 126449 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.15→2.18 Å / % possible all: 98.4 |
-Phasing
Phasing MR | Rfactor: 36.2 / Cor.coef. Fo:Fc: 68.5 / Cor.coef. Io to Ic: 66.7
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.254 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.064 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.145→2.201 Å / Total num. of bins used: 20
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