+Open data
-Basic information
Entry | Database: PDB / ID: 1mz6 | ||||||
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Title | Trypanosoma rangeli sialidase in complex with the inhibitor DANA | ||||||
Components | sialidaseNeuraminidase | ||||||
Keywords | hydrolase / hydrolase inhibitor / inibitor complex / trypanosomal sialidase / sialyltransferase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Buschiazzo, A. / Tavares, G.A. / Campetella, O. / Spinelli, S. / Cremona, M.L. / Paris, G. / Amaya, M.F. / Frasch, A.C.C. / Alzari, P.M. | ||||||
Citation | Journal: Embo J. / Year: 2000 Title: Structural basis of sialyltransferase activity in trypanosomal sialidases Authors: Buschiazzo, A. / Tavares, G.A. / Campetella, O. / Spinelli, S. / Cremona, M.L. / Paris, G. / Amaya, M.F. / Frasch, A.C.C. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mz6.cif.gz | 127.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mz6.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 1mz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/1mz6 ftp://data.pdbj.org/pub/pdb/validation_reports/mz/1mz6 | HTTPS FTP |
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-Related structure data
Related structure data | 1mz5SC S: Starting model for refinement C: citing same article (ref.) |
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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: 69705.445 Da / Num. of mol.: 1 / Fragment: mature sialidase / Source method: isolated from a natural source / Source: (natural) Trypanosoma rangeli (eukaryote) / References: UniProt: O44049, exo-alpha-sialidase | ||||
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#2: Sugar | ChemComp-NAG / #3: Sugar | ChemComp-DAN / | #4: 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: 2.7 Å3/Da / Density % sol: 54.41 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG-8000, ammonium sulfate, morpholinoethanesulfonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||
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: D41A / Wavelength: 1.375 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→15 Å / Num. all: 17063 / Num. obs: 17063 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.138 |
Reflection shell | Resolution: 2.9→2.98 Å / Rsym value: 0.306 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. measured all: 112960 / Rmerge(I) obs: 0.138 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.306 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Unliganded T. rangeli sialidase 1MZ5 Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.776 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 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: 22.262 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.973 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 16275 / Rfactor Rfree: 0.314 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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