+Open data
-Basic information
Entry | Database: PDB / ID: 5ayi | ||||||
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Title | Crystal structure of GH1 Beta-glucosidase TD2F2 N223Q mutant | ||||||
Components | BETA-GLUCOSIDASE | ||||||
Keywords | HYDROLASE / TIM BARREL | ||||||
Function / homology | Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / beta-D-glucopyranose Function and homology information | ||||||
Biological species | metagenomes (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 5ayi.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ayi.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ayi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/5ayi ftp://data.pdbj.org/pub/pdb/validation_reports/ay/5ayi | HTTPS FTP |
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-Related structure data
Related structure data | 3wh5SC 3wh6C 3wh7C 3wh8C 5aybC C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 50860.883 Da / Num. of mol.: 1 / Mutation: N223Q 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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#4: Sugar | ChemComp-BGC / |
-Non-polymers , 4 types, 382 molecules
#2: Chemical | ChemComp-NHE / | ||
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#3: Chemical | ChemComp-NA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLN REPRESENT ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. RESIDUE 223 GLN REPRESENT MUTATION N223Q. |
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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: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging 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: Nov 8, 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: 1.85→50 Å / Num. obs: 40537 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WH5 Resolution: 1.85→45.97 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.411 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.105 / 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: 13.71 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→45.97 Å
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Refine LS restraints |
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