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Yorodumi- PDB-2xzi: THE ASPERGILLUS FUMIGATUS SIALIDASE IS A KDNASE: STRUCTURAL AND M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xzi | |||||||||
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Title | THE ASPERGILLUS FUMIGATUS SIALIDASE IS A KDNASE: STRUCTURAL AND MECHANISTIC INSIGHTS | |||||||||
Components | EXTRACELLULAR SIALIDASE/NEURAMINIDASE, PUTATIVE | |||||||||
Keywords | HYDROLASE | |||||||||
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 / SYNCHROTRON / OTHER / Resolution: 1.45 Å | |||||||||
Authors | Telford, J.C. / Yeung, J.H.F. / Kiefel, M.J. / Watts, A.G. / Hader, S. / Chan, J. / Bennet, A.J. / 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.F. / 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 | 2xzi.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xzi.ent.gz | 148.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/2xzi ftp://data.pdbj.org/pub/pdb/validation_reports/xz/2xzi | HTTPS FTP |
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-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
-Protein / Sugars , 2 types, 6 molecules AB
#1: Protein | Mass: 42117.703 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-406 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q4WQS0, exo-alpha-sialidase #2: Sugar | ChemComp-KDM / |
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-Non-polymers , 4 types, 1163 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NO2 / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→37.3 Å / Num. obs: 143277 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.3 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.45→37.31 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.093 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / 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: 12.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→37.31 Å
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