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Yorodumi- PDB-2ags: Trypanosoma rangeli Sialidase in Complex with 2-Keto-3-deoxy-D-gl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ags | ||||||
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Title | Trypanosoma rangeli Sialidase in Complex with 2-Keto-3-deoxy-D-glycero-D-galacto-2,3-difluoro-nononic acid (2,3-difluoro-KDN) | ||||||
Components | sialidase | ||||||
Keywords | HYDROLASE / beta-propeller / covalent enzyme-intermediate complex / beta-sandwich | ||||||
Function / homology | Function and homology information 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 | Trypanosoma rangeli (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||
Authors | Amaya, M.F. / Alzari, P.M. / Buschiazzo, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural and Kinetic Analysis of Two Covalent Sialosyl-Enzyme Intermediates on Trypanosoma rangeli Sialidase. Authors: Watts, A.G. / Oppezzo, P. / Withers, S.G. / Alzari, P.M. / Buschiazzo, A. | ||||||
History |
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Remark 999 | SEQUENCE Authors indicate that the aminoacid sequence in the sequence database is incorrect |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ags.cif.gz | 157.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ags.ent.gz | 118.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ags.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ags_validation.pdf.gz | 776.1 KB | Display | wwPDB validaton report |
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Full document | 2ags_full_validation.pdf.gz | 783.9 KB | Display | |
Data in XML | 2ags_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 2ags_validation.cif.gz | 51 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/2ags ftp://data.pdbj.org/pub/pdb/validation_reports/ag/2ags | HTTPS FTP |
-Related structure data
Related structure data | 2a75SC 2fhrC 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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Details | The biological unit is a monomer |
-Components
#1: Protein | Mass: 71205.203 Da / Num. of mol.: 1 / Fragment: residues 23-660 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma rangeli (eukaryote) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O44049, exo-alpha-sialidase | ||||
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#2: Chemical | #3: Sugar | ChemComp-FKD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, ammonium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2005 / Details: toroidal mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35 Å / Num. all: 81374 / Num. obs: 81374 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.7→1.79 Å / % possible obs: 93.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.8 / Num. measured obs: 11177 / Num. unique all: 11177 / Rsym value: 0.247 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2A75 Resolution: 1.7→35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.62 / SU ML: 0.055 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.09 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.827 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→35 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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