+Open data
-Basic information
Entry | Database: PDB / ID: 5ayb | ||||||
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Title | Crystal structure of GH1 Beta-Glucosidase TD2F2 N223G mutant | ||||||
Components | BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / TIM BARREL | ||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Function and homology information | ||||||
Biological species | metagenomes (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Jo, T. / Manninen, J.A. / Matsuzawa, T. / Uchiyama, T. / Yaoi, K. / Arakawa, T. / Fushinobu, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2016 Title: Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity, and transglycosylation activity of metagenomic beta-glucosidase Td2F2 Authors: Matsuzawa, T. / Jo, T. / Uchiyama, T. / Manninen, J.A. / Arakawa, T. / Miyazaki, K. / Fushinobu, S. / Yaoi, K. #1: Journal: J. Biol. Chem. / Year: 2013 Title: Characterization of a novel beta-glucosidase from a compost microbial metagenome with strong transglycosylation activity. Authors: Uchiyama, T. / Miyazaki, K. / Yaoi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ayb.cif.gz | 109.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ayb.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ayb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayb ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayb | HTTPS FTP |
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-Related structure data
Related structure data | 3wh5SC 3wh6C 3wh7C 3wh8C 5ayiC 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
#1: Protein | Mass: 50789.805 Da / Num. of mol.: 1 / Mutation: N223G Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenomes (others) / Plasmid: PJTTD2F2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: beta-glucosidase | ||||
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#2: Chemical | ChemComp-NHE / | ||||
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLY REPRESENT ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLY REPRESENT MUTATION N223G. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.2M K/NA TARTRATE, 0.1M NA-CHES, 0.2M LI2SO4, PH 8.5 |
-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 210 / Detector: CCD / Date: Jun 22, 2014 |
Radiation | Monochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 43580 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WH5 Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.96 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.091 / 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: 19.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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