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Yorodumi- PDB-3pjq: Trypanosoma cruzi trans-sialidase-like inactive isoform (includin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pjq | |||||||||
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Title | Trypanosoma cruzi trans-sialidase-like inactive isoform (including the natural mutation Tyr342His) in complex with lactose | |||||||||
Components | Trans-sialidase | |||||||||
Keywords | SUGAR BINDING PROTEIN / beta-propeller / lectin / similar to actve trans-sialidases / lactose | |||||||||
Function / homology | Function and homology information exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | |||||||||
Authors | Oppezzo, P. / Baraibar, M. / Obal, G. / Pritsch, O. / Alzari, P.M. / Buschiazzo, A. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2011 Title: Crystal structure of an enzymatically inactive trans-sialidase-like lectin from Trypanosoma cruzi: the carbohydrate binding mechanism involves residual sialidase activity. Authors: Oppezzo, P. / Obal, G. / Baraibar, M.A. / Pritsch, O. / Alzari, P.M. / Buschiazzo, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pjq.cif.gz | 261.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pjq.ent.gz | 210.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pj/3pjq ftp://data.pdbj.org/pub/pdb/validation_reports/pj/3pjq | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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-Components
#1: Protein | Mass: 71364.234 Da / Num. of mol.: 1 / Fragment: unp residues 2-635 / Mutation: N58F,Y342H,S495K,V496G,E520K,D593G,I597D,H599R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / Strain (production host): Top10f / References: UniProt: Q26966, exo-alpha-sialidase |
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose |
#3: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT THE RESIDUES 262, 342, 476, 484 AND 558 ARE NOT CORRECT AT THE CORRESPONDING ...AUTHORS STATE THAT THE RESIDUES 262, 342, 476, 484 AND 558 ARE NOT CORRECT AT THE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: microseeding in 10% PEG 4000, 100mM Tris.HCl, 5% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2004 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.95→51.778 Å / Num. all: 29944 / Num. obs: 29944 / % possible obs: 71.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.2439 / WRfactor Rwork: 0.185 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8034 / SU B: 15.939 / SU ML: 0.196 / SU R Cruickshank DPI: 0.0758 / SU Rfree: 0.0531 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.84 Å2 / Biso mean: 38.3444 Å2 / Biso min: 15.2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.096→2.15 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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