+Open data
-Basic information
Entry | Database: PDB / ID: 2zx8 | ||||||
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Title | alpha-L-fucosidase complexed with inhibitor, F10-2C-O | ||||||
Components | Alpha-L-fucosidase, putative | ||||||
Keywords | HYDROLASE / Tim Barrel | ||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Wu, H.-J. / Ko, T.-P. / Ho, C.-W. / Lin, C.-H. / Wang, A.H.-J. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zx8.cif.gz | 198.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zx8.ent.gz | 158.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zx8_validation.pdf.gz | 1021.3 KB | Display | wwPDB validaton report |
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Full document | 2zx8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2zx8_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 2zx8_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zx8 ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zx8 | HTTPS FTP |
-Related structure data
Related structure data | 2zwzSC 2zx5C 2zx6C 2zx7C 2zx9C 2zxaC 2zxbC 2zxdC 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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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.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYE2, alpha-L-fucosidase #2: Chemical | #3: 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: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 14% PEG 5000 MME, 0.1M Tris-HCl, pH 8.2, 8% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled, Fixed-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: 2.33→30 Å / Num. all: 45228 / Num. obs: 45183 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4452 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB enrty 2zwz Resolution: 2.33→27.84 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 54.829 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 85.38 Å2 / Biso mean: 41.732 Å2 / Biso min: 17.65 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.33→27.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.41 Å / Rfactor Rfree error: 0.0344
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