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- PDB-2xib: 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: 2xib | ||||||
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Title | CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH DEOXYFUCONOJIRIMYCIN | ||||||
![]() | ALPHA-L-FUCOSIDASE | ||||||
![]() | HYDROLASE / FUCOSIDASE / METAL BINDING / INHIBITORS | ||||||
Function / homology | ![]() alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lammerts van Bueren, A. / Popat, S.D. / Lin, C.H. / Davies, G.J. | ||||||
![]() | ![]() Title: Structural and Thermodynamic Analyses of Alpha-L-Fucosidase Inhibitors. Authors: Lammerts Van Bueren, A. / Popat, S.D. / Lin, C.H. / 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 | ![]() | 369.6 KB | Display | ![]() |
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PDB format | ![]() | 302 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 511.6 KB | Display | ![]() |
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Full document | ![]() | 525.9 KB | Display | |
Data in XML | ![]() | 68 KB | Display | |
Data in CIF | ![]() | 95.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xiiC ![]() 2wvvS 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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 52410.367 Da / Num. of mol.: 4 / Fragment: RESIDUES 32-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 734 molecules ![](data/chem/img/DFU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DFU / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.88 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. obs: 98203 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WVV Resolution: 2.2→34.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.834 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.211 / 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: 22.774 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→34.75 Å
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Refine LS restraints |
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