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- PDB-2xii: 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: 2xii | ||||||
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Title | CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH AN EXTENDED 9-FLUORENONE IMINOSUGAR INHIBITOR | ||||||
![]() | ALPHA-L-FUCOSIDASE | ||||||
![]() | HYDROLASE / FUCOSE | ||||||
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 | ![]() | 204.9 KB | Display | ![]() |
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PDB format | ![]() | 162.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 39.8 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xibC ![]() 2wvtS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52410.367 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, 32-484 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 5 types, 705 molecules ![](data/chem/img/TYR.gif)
![](data/chem/img/TA9.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TA9.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % / Description: NONE |
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Crystal grow | Details: 20% PEG-6000, 0.15M AMMONIUM SULFATE, 0.1M IMIDAZOLE PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45 Å / Num. obs: 92257 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WVT Resolution: 1.8→45.15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.079 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.123 / 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: 20.537 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→45.15 Å
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Refine LS restraints |
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