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Yorodumi- PDB-1ms0: Monoclinic form of Trypanosoma cruzi trans-sialidase, in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ms0 | |||||||||
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Title | Monoclinic form of Trypanosoma cruzi trans-sialidase, in complex with 3-deoxy-2,3-dehydro-N-acetylneuraminic acid (DANA)and lactose | |||||||||
Components | trans-sialidase | |||||||||
Keywords | HYDROLASE / transglycosylation / beta-propeller / protein-carbohydrate interactions / sialidase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 1ms0.cif.gz | 261.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ms0.ent.gz | 215.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ms0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1ms0 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1ms0 | HTTPS FTP |
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-Related structure data
Related structure data | 1mr5C 1ms1C 1ms3C 1ms4C 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): DH5a-FT References: UniProt: Q26964, UniProt: Q26966*PLUS, exo-alpha-sialidase #2: Polysaccharide | #3: Sugar | #4: 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: 2.76 Å3/Da / Density % sol: 55.41 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, TrisHCl, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Mar 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 66109 / Num. obs: 66109 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.103 |
Reflection shell | Resolution: 2.5→2.54 Å / Rsym value: 0.471 / % possible all: 96.5 |
Reflection | *PLUS Redundancy: 3.3 % / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 96.5 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb id 1MZ5 Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / 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: 24.571 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.563 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 15 Å / Num. reflection obs: 49558 / % reflection Rfree: 5 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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