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- PDB-2wvt: Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wvt | ||||||
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Title | Crystal structure of an alpha-L-fucosidase GH29 from Bacteroides thetaiotaomicron in complex with a novel iminosugar fucosidase inhibitor | ||||||
![]() | ALPHA-L-FUCOSIDASE | ||||||
![]() | HYDROLASE / ALPHA-L-FUCOSE / GLYCOSIDE HYDROLASE FAMILY 29 | ||||||
Function / homology | ![]() alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lammerts van Bueren, A. / Ardevol, A. / Fayers-Kerr, J. / Luo, B. / Zhang, Y. / Sollogoub, M. / Bleriot, Y. / Rovira, C. / Davies, G.J. | ||||||
![]() | ![]() Title: Analysis of the Reaction Coordinate of Alpha-L-Fucosidases: A Combined Structural and Quantum Mechanical Approach. Authors: Lammerts Van Bueren, A. / Ardevol, A. / Fayers-Kerr, J. / Luo, B. / Zhang, Y. / Sollogoub, M. / Bleriot, Y. / Rovira, C. / Davies, G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.3 KB | Display | ![]() |
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PDB format | ![]() | 156.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.6 KB | Display | ![]() |
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Full document | ![]() | 480.8 KB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 54 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wvsC ![]() 2wvuC ![]() 2wvvSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51331.121 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-473 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Plasmid: PET28 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-IMD / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.87 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 18, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48 Å / Num. obs: 93456 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7 |
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Processing
Software | Name: REFMAC / Version: 5.5.0102 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WVV Resolution: 1.8→90.93 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.471 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.158 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→90.93 Å
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Refine LS restraints |
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