+Open data
-Basic information
Entry | Database: PDB / ID: 1n1v | ||||||
---|---|---|---|---|---|---|---|
Title | Trypanosoma rangeli sialidase in complex with DANA | ||||||
Components | SialidaseNeuraminidase | ||||||
Keywords | HYDROLASE / BETA PROPELLER / LECTIN-LIKE FOLD | ||||||
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: 2.1 Å | ||||||
Authors | Amaya, M.F. / Buschiazzo, A. / Nguyen, T. / Alzari, P.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The high resolution structures of free and inhibitor-bound Trypanosoma rangeli sialidase and its comparison with T. cruzi trans-sialidase Authors: Amaya, M.F. / Buschiazzo, A. / Nguyen, T. / Alzari, P.M. #1: 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. / Alzari, P.M. | ||||||
History |
| ||||||
Remark 999 | sequence The author maintains that the sequence in the sequence database is incorrect. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n1v.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n1v.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n1v ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n1v | HTTPS FTP |
---|
-Related structure data
Related structure data | 1n1sSC 1n1tC 1n1yC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 69912.727 Da / Num. of mol.: 1 / Fragment: residue 23-660 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma rangeli (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: O44049, exo-alpha-sialidase | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Sugar | ChemComp-DAN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.11 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG-8000, sodium cacodylate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 39923 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.052 |
Reflection shell | Resolution: 2.1→2.14 Å / Rsym value: 0.208 / % possible all: 52.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 116221 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 52.3 % / Rmerge(I) obs: 0.208 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1n1s Resolution: 2.1→14.94 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 24.149 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→14.94 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.153 Å / Total num. of bins used: 20 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.178 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.14 Å |