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- PDB-1dil: SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dil | |||||||||
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Title | SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EPANA INHIBITORS | |||||||||
![]() | SIALIDASE | |||||||||
![]() | GLYCOSIDASE / HYDROLASE | |||||||||
Function / homology | ![]() exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Garman, E.F. / Crennell, S.C. / Vimr, E.R. / Laver, W.G. / Taylor, G.L. | |||||||||
![]() | ![]() Title: The structures of Salmonella typhimurium LT2 neuraminidase and its complexes with three inhibitors at high resolution. Authors: Crennell, S.J. / Garman, E.F. / Philippon, C. / Vasella, A. / Laver, W.G. / Vimr, E.R. / Taylor, G.L. #1: ![]() Title: Crystal Structure of a Bacterial Sialidase (from Salmonella Typhimurium Lt2) Shows the Same Fold as an Influenza Virus Neuraminidase Authors: Crennell, S.J. / Garman, E.F. / Laver, W.G. / Vimr, E.R. / Taylor, G.L. #2: ![]() Title: Purification, Crystallization and Preliminary Crystallographic Study of Neuraminidase from Vibrio Cholerae and Salmonella Typhimurium Lt2 Authors: Taylor, G. / Vimr, E. / Garman, E. / Laver, G. #3: ![]() Title: Phosphonic-Acid Analogues of the N-Acetyl-2-Deoxyneuraminic Acids: Synthesis and Inhibition of Vibrio Cholerae Sialidase Authors: Wallimann, K. / Vasella, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.5 KB | Display | ![]() |
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PDB format | ![]() | 68.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 528.8 KB | Display | ![]() |
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Full document | ![]() | 536.7 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dimC ![]() 2silC ![]() 2simSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41991.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-EQP / ( |
#3: Sugar | ChemComp-AXP / ( |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 17, 1993 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. obs: 27890 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 5.7 / % possible all: 96.9 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. measured all: 100231 |
Reflection shell | *PLUS Lowest resolution: 2 Å / Rmerge(I) obs: 0.088 |
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Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE MAP Starting model: PDB ENTRY 2SIM Resolution: 1.9→6 Å / σ(F): 0 Details: OCCUPANCY OF AXIAL PHOSPHONATE (APANA) 0.6. OCCUPANCY OF EQUATORIAL PHOSPHONATE ANOMER (EPANA) 0.4. 5% IMPURITY OF EPANA IN APANA, BUT KI OF EPANA SMALLER THAN FOR APANA, SO A LARGER ...Details: OCCUPANCY OF AXIAL PHOSPHONATE (APANA) 0.6. OCCUPANCY OF EQUATORIAL PHOSPHONATE ANOMER (EPANA) 0.4. 5% IMPURITY OF EPANA IN APANA, BUT KI OF EPANA SMALLER THAN FOR APANA, SO A LARGER PROPORTION OF EPANA IN CRYSTAL THAN WOULD BE EXPECTED FROM IMPURITY. DETAILS OF OCCUPANCY DETERMINATION IN J.MOL.BIOL. V259 (2) 264-280 (1996).
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Displacement parameters | Biso mean: 15.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: STNA_APANA.PAR / Topol file: STNA_APANA.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |