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Yorodumi- PDB-2fhr: Trypanosoma Rangeli Sialidase In Complex With 2,3- Difluorosialic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fhr | ||||||
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Title | Trypanosoma Rangeli Sialidase In Complex With 2,3- Difluorosialic Acid (Covalent Intermediate) | ||||||
Components | sialidaseNeuraminidase | ||||||
Keywords | HYDROLASE / BETA-PROPELLER / COVALENT ENZYME-INTERMEDIATE COMPLEX / BETA-SANDWICH | ||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / metabolic process Similarity search - Function | ||||||
Biological species | Trypanosoma rangeli (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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 sequence in the database is incorrect |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fhr.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fhr.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 2fhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/2fhr ftp://data.pdbj.org/pub/pdb/validation_reports/fh/2fhr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a monomer and corresponds to the monomer present in the ASU |
-Components
#1: Protein | Mass: 71205.203 Da / Num. of mol.: 1 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: GenBank: 2894810, UniProt: O44049*PLUS, exo-alpha-sialidase | ||||||
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#2: Chemical | #3: Sugar | ChemComp-FSI / | #4: Chemical | ChemComp-GOL / | #5: 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: 2.76 Å3/Da / Density % sol: 55.51 % |
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Crystal grow | Temperature: 291 K / pH: 6.5 Details: PEG 8000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979158 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 2, 2003 |
Radiation | Monochromator: SI 311 CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979158 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→72.17 Å / Num. obs: 36222 / % possible obs: 89.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / Rsym value: 0.34 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→29.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.365 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.212 / Stereochemistry target values: ENGH & HUBER Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TLS PARAMETERS HAVE BEEN REFINED
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.16 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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