+Open data
-Basic information
Entry | Database: PDB / ID: 2xcy | ||||||
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Title | Crystal structure of Aspergillus fumigatus sialidase | ||||||
Components | EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE | ||||||
Function / homology | Function and homology information exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.84 Å | ||||||
Authors | Telford, J.C. / Yeung, J. / Xu, G. / Bennet, A. / Moore, M.M. / Taylor, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Aspergillus Fumigatus Sialidase is a Kdnase: Structural and Mechanistic Insights. Authors: Telford, J.C. / Yeung, J.H. / Xu, G. / Kiefel, M.J. / Watts, A.G. / Hader, S. / Chan, J. / Bennet, A.J. / Moore, M.M. / Taylor, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xcy.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xcy.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xcy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xcy_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 2xcy_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 2xcy_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 2xcy_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/2xcy ftp://data.pdbj.org/pub/pdb/validation_reports/xc/2xcy | HTTPS FTP |
-Related 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
#1: Protein | Mass: 42352.176 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4WQS0, exo-alpha-sialidase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 2.37 Å3/Da / Density % sol: 48 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD / Detector: CCD / Date: Feb 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→12.4 Å / Num. obs: 59980 / % possible obs: 84.2 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.84→1.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.2 / % possible all: 64.8 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.84→12.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.23 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 11.755 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→12.4 Å
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Refine LS restraints |
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