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Yorodumi- PDB-4wsj: Crystal structure of a bacterial fucodiase in complex with 1-((1R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wsj | |||||||||
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Title | Crystal structure of a bacterial fucodiase in complex with 1-((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)ethan-1-one | |||||||||
Components | Alpha-L-fucosidase | |||||||||
Keywords | HYDROLASE / Fucosidase Complex Covalent Inhibitor | |||||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | |||||||||
Authors | Davies, G.J. / Wright, D.W. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Chem Sci / Year: 2015 Title: In vitroandin vivocomparative and competitive activity-based protein profiling of GH29 alpha-l-fucosidases. Authors: Jiang, J. / Kallemeijn, W.W. / Wright, D.W. / van den Nieuwendijk, A.M.C.H. / Rohde, V.C. / Folch, E.C. / van den Elst, H. / Florea, B.I. / Scheij, S. / Donker-Koopman, W.E. / Verhoek, M. / ...Authors: Jiang, J. / Kallemeijn, W.W. / Wright, D.W. / van den Nieuwendijk, A.M.C.H. / Rohde, V.C. / Folch, E.C. / van den Elst, H. / Florea, B.I. / Scheij, S. / Donker-Koopman, W.E. / Verhoek, M. / Li, N. / Schurmann, M. / Mink, D. / Boot, R.G. / Codee, J.D.C. / van der Marel, G.A. / Davies, G.J. / Aerts, J.M.F.G. / Overkleeft, H.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wsj.cif.gz | 394.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wsj.ent.gz | 315.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/4wsj ftp://data.pdbj.org/pub/pdb/validation_reports/ws/4wsj | HTTPS FTP |
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-Related structure data
Related structure data | 4wskC 4jfvS 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 51523.309 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2970 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A3I4 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-3U3 / #4: 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: 2.46 Å3/Da / Density % sol: 50.09 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2014 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.64→93.49 Å / Num. obs: 238023 / % possible obs: 98.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.2 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JFV Resolution: 1.64→93.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1946 / WRfactor Rwork: 0.1645 / FOM work R set: 0.8595 / SU B: 1.967 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0858 / SU Rfree: 0.0862 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.086 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.39 Å2 / Biso mean: 25.202 Å2 / Biso min: 10.76 Å2
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Refinement step | Cycle: final / Resolution: 1.64→93.49 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.64→1.683 Å / Total num. of bins used: 20
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