+Open data
-Basic information
Entry | Database: PDB / ID: 1ms3 | ||||||
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Title | Monoclinic form of Trypanosoma cruzi trans-sialidase | ||||||
Components | trans-sialidase | ||||||
Keywords | HYDROLASE / transglycosylation / beta-propeller / protein-carbohydrate interactions / sialidase | ||||||
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: 1.65 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 | 1ms3.cif.gz | 272.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ms3.ent.gz | 225.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ms3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ms3_validation.pdf.gz | 378.8 KB | Display | wwPDB validaton report |
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Full document | 1ms3_full_validation.pdf.gz | 392.7 KB | Display | |
Data in XML | 1ms3_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 1ms3_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/1ms3 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/1ms3 | HTTPS FTP |
-Related structure data
Related structure data | 1mr5C 1ms0C 1ms1C 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: 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: 2.47 Å3/Da / Density % sol: 50.19 % | ||||||||||||||||||||||||||||||
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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 291K | ||||||||||||||||||||||||||||||
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: LURE / Beamline: DW32 / Wavelength: 0.966 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 166779 / Num. obs: 166779 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.09 |
Reflection shell | Resolution: 1.65→1.68 Å / Rsym value: 0.393 / % possible all: 72.8 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 72.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb id 1MZ5 Resolution: 1.65→14.97 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / 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: 20.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→14.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.66 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.163 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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