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Yorodumi- PDB-7wdr: Crystal structures of MeBglD2 in complex with various saccharides -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wdr | ||||||
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Title | Crystal structures of MeBglD2 in complex with various saccharides | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / glycoside hydrolase family 1 | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Watanabe, M. / Matsuzawa, T. / Nakamichi, Y. / Akita, H. / Yaoi, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2022 Title: Crystal structure of metagenomic beta-glycosidase MeBglD2 in complex with various saccharides Authors: Matsuzawa, T. / Watanabe, M. / Nakamichi, Y. / Akita, H. / Yaoi, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wdr.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wdr.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 7wdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/7wdr ftp://data.pdbj.org/pub/pdb/validation_reports/wd/7wdr | HTTPS FTP |
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-Related structure data
Related structure data | 7wdoC 7wdpC 7wdsC 7wdvC 5xgzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 52127.074 Da / Num. of mol.: 1 / Mutation: E356A Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E1FFN6, beta-glucosidase | ||||||
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#2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl buffer (pH 8.5), 1.2 M lithium sulfate, 0.01 M nickel chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 46907 / % possible obs: 99.5 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.777 / Num. unique obs: 2294 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XGZ Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.447 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.143 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 56.606 Å2
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Refinement step | Cycle: 1 / Resolution: 2→19.99 Å
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Refine LS restraints |
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