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Yorodumi- PDB-5xxn: Crystal Structure of mutant (D286N) beta-glucosidase from Bactero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xxn | |||||||||
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Title | Crystal Structure of mutant (D286N) beta-glucosidase from Bacteroides thetaiotaomicron in complex with sophorose | |||||||||
Components | Periplasmic beta-glucosidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase family 3 / beta-glucosidase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Nakajima, M. / Ishiguro, R. / Tanaka, N. / Abe, K. / Maeda, T. / Miyanaga, A. / Takahashi, Y. / Sugimono, N. / Nakai, H. / Taguchi, H. | |||||||||
Citation | Journal: FEBS Lett. / Year: 2017 Title: Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase. Authors: Ishiguro, R. / Tanaka, N. / Abe, K. / Nakajima, M. / Maeda, T. / Miyanaga, A. / Takahashi, Y. / Sugimoto, N. / Nakai, H. / Taguchi, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xxn.cif.gz | 313.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xxn.ent.gz | 249.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xxn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/5xxn ftp://data.pdbj.org/pub/pdb/validation_reports/xx/5xxn | HTTPS FTP |
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-Related structure data
Related structure data | 5xxlSC 5xxmC 5xxoC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 84017.555 Da / Num. of mol.: 2 / Mutation: D286N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3567 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A1U1 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-GLC / | |
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-Non-polymers , 4 types, 769 molecules
#3: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | ChemComp-PG4 / | #7: 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: 46.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 2, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 94130 / % possible obs: 96.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.05→2.09 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XXL Resolution: 2.05→46.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.003 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.173 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.481 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→46.74 Å
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