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- PDB-4wsk: Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4wsk | ||||||
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Title | Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)methanone | ||||||
![]() | Alpha-L-fucosidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Davies, G.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 391.3 KB | Display | ![]() |
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PDB format | ![]() | 313.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4wsjC ![]() 4jfvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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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: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 0
NCS ensembles :
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Components
#1: Protein | ![]() Mass: 54129.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2970 / Production host: ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | #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: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M imidazole pH 7.0, 0.2 M ammonium sulfate, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.92→53.2 Å / Num. obs: 199312 / % possible obs: 96.9 % / Redundancy: 4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.058 / Net I/σ(I): 7 / Num. measured all: 579846 / Scaling rejects: 80 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4JFV Resolution: 1.92→97.89 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2384 / WRfactor Rwork: 0.1871 / FOM work R set: 0.8148 / SU B: 4.222 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1623 / SU Rfree: 0.1533 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 96.86 Å2 / Biso mean: 31.583 Å2 / Biso min: 11.38 Å2
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Refinement step | Cycle: final / Resolution: 1.92→97.89 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: 1.92→1.97 Å / Total num. of bins used: 20
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