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Yorodumi- PDB-1dim: SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH EPANA INHIBITOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dim | ||||||
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Title | SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH EPANA INHIBITOR | ||||||
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: 1.6 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dim.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dim.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 1dim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1dim ftp://data.pdbj.org/pub/pdb/validation_reports/di/1dim | HTTPS FTP |
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-Related structure data
Related structure data | 1dilC 2silC 2simSC 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: 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 |
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#2: Chemical | ChemComp-K / |
#3: Sugar | ChemComp-EQP / ( |
#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: 2.13 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: 289 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Dec 5, 1992 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→10 Å / Num. obs: 12091 / % possible obs: 89.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 6.8 / % possible all: 87.8 |
Reflection | *PLUS Lowest resolution: 9999 Å / Num. obs: 43572 / Num. measured all: 189373 |
Reflection shell | *PLUS Lowest resolution: 1.7 Å |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE MAP Starting model: PDB ENTRY 2SIM Resolution: 1.6→6 Å / σ(F): 0 /
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Displacement parameters | Biso mean: 14.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→6 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |