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Open data
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Basic information
Entry | Database: PDB / ID: 2zxd | ||||||
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Title | alpha-L-fucosidase complexed with inhibitor, iso-6FNJ | ||||||
![]() | Alpha-L-fucosidase, putative | ||||||
![]() | HYDROLASE / Tim Barrel | ||||||
Function / homology | ![]() alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, H.-J. / Ko, T.-P. / Ho, C.-W. / Lin, C.-H. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Structural basis of alpha-fucosidase inhibition by iminocyclitols with K(i) values in the micro- to picomolar range. Authors: Wu, H.J. / Ho, C.W. / Ko, T.P. / Popat, S.D. / Lin, C.H. / Wang, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.1 KB | Display | ![]() |
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PDB format | ![]() | 160.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463 KB | Display | ![]() |
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Full document | ![]() | 478.2 KB | Display | |
Data in XML | ![]() | 39.1 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zwzSC ![]() 2zx5C ![]() 2zx6C ![]() 2zx7C ![]() 2zx8C ![]() 2zx9C ![]() 2zxaC ![]() 2zxbC 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 53100.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 14% PEG 5000 MME, 0.1M Tris-HCl, pH 7.8, 5% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2008 Details: 1-m-long platimun-coated bent-cylinder focusing mirror |
Radiation | Monochromator: fix-exit double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 58368 / Num. obs: 58320 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 37.5 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5773 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB enrty 2zwz Resolution: 2.15→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 66.272 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 77.99 Å2 / Biso mean: 35.747 Å2 / Biso min: 15.87 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Rfactor Rfree error: 0.0503
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