+Open data
-Basic information
Entry | Database: PDB / ID: 1ms4 | ||||||
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Title | Triclinic form of Trypanosoma cruzi trans-sialidase | ||||||
Components | trans-sialidase | ||||||
Keywords | HYDROLASE / sialidase / trans-glycosylation / beta-propeller / protein-carbohydrate interaction | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Buschiazzo, A. / Amaya, M.F. / Cremona, M.L. / Frasch, A.C. / Alzari, P.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis Authors: Buschiazzo, A. / Amaya, M.F. / Cremona, M.L. / Frasch, A.C. / Alzari, P.M. | ||||||
History |
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Remark 999 | sequence Author indicates 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 | 1ms4.cif.gz | 244.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ms4.ent.gz | 203.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ms4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ms4_validation.pdf.gz | 379.3 KB | Display | wwPDB validaton report |
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Full document | 1ms4_full_validation.pdf.gz | 392.8 KB | Display | |
Data in XML | 1ms4_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 1ms4_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1ms4 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1ms4 | HTTPS FTP |
-Related structure data
Related structure data | 1mr5C 1ms0C 1ms1C 1ms3C 1ms5C 1ms8C 1ms9C 1mz5S C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 71389.258 Da / Num. of mol.: 2 / Fragment: enzymatic globular core / Mutation: N58F, 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): DH5alpha-FT References: UniProt: Q26964, UniProt: Q26966*PLUS, exo-alpha-sialidase #2: 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: 2.3 Å3/Da / Density % sol: 46.46 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Tris.HCl, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 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: May 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→38.633 Å / Num. all: 60767 / Num. obs: 60767 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.059 |
Reflection shell | Resolution: 2.21→2.33 Å / Rsym value: 0.094 / % possible all: 86.7 |
Reflection | *PLUS Redundancy: 1.9 % / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 86.7 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 5.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb id 1MZ5 Resolution: 2.21→34.92 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.859 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 mean: 17.414 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→34.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.212→2.269 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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