[English] 日本語
Yorodumi- PDB-1dil: SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dil | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EPANA INHIBITORS | |||||||||
Components | SIALIDASENeuraminidase | |||||||||
Keywords | GLYCOSIDASE / HYDROLASE | |||||||||
Function / homology | Function and homology information ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / 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 | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE MAP / Resolution: 1.9 Å | |||||||||
Authors | Garman, E.F. / Crennell, S.C. / Vimr, E.R. / Laver, W.G. / Taylor, G.L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 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: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 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: Journal: J.Mol.Biol. / Year: 1992 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: Journal: Helv.Chim.Acta / Year: 1990 Title: Phosphonic-Acid Analogues of the N-Acetyl-2-Deoxyneuraminic Acids: Synthesis and Inhibition of Vibrio Cholerae Sialidase Authors: Wallimann, K. / Vasella, A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dil.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dil.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1dil ftp://data.pdbj.org/pub/pdb/validation_reports/di/1dil | HTTPS FTP |
---|
-Related structure data
Related structure data | 1dimC 2silC 2simSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41991.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Description: RESIDUE MET 1 WAS EXCISED BY ESCHERICHIA COLI / Gene: NANH / Variant: TA263, PROTOTROPH / Plasmid: PSX62 / Gene (production host): NANH / Production host: Escherichia coli (E. coli) / References: UniProt: P29768, exo-alpha-sialidase |
---|---|
#2: Sugar | ChemComp-EQP / ( |
#3: Sugar | ChemComp-AXP / ( |
#4: Chemical | ChemComp-K / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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).
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: STNA_APANA.PAR / Topol file: STNA_APANA.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |