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Yorodumi- PDB-2xii: CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES ... -
+Open data
-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 | ||||||
Components | ALPHA-L-FUCOSIDASE | ||||||
Keywords | HYDROLASE / FUCOSE | ||||||
Function / homology | Function and homology information alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome Similarity search - Function | ||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Lammerts van Bueren, A. / Popat, S.D. / Lin, C.H. / Davies, G.J. | ||||||
Citation | Journal: Chembiochem / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xii.cif.gz | 204.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xii.ent.gz | 162.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xii_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2xii_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xii_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 2xii_validation.cif.gz | 59.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xii ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xii | HTTPS FTP |
-Related structure data
Related structure data | 2xibC 2wvtS 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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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.) BACTEROIDES THETAIOTAOMICRON (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A3I4, alpha-L-fucosidase |
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-Non-polymers , 5 types, 705 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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