[English] 日本語
Yorodumi- PDB-2sil: THE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND IT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2sil | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND ITS COMPLEX WITH A TRANSITION STATE ANALOGUE AT 1.6 ANGSTROMS RESOLUTION | |||||||||
Components | SIALIDASENeuraminidase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information 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 | Salmonella typhimurium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Taylor, G.L. / Crennell, S.J. / Garman, E.F. / Vimr, E.R. / Laver, W.G. | |||||||||
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, Crystallisation and Preliminary Crystallographic Study of Neuraminidase from Vibrio Cholerae and Salmonella Typhimurium Authors: Taylor, G.L. / Vimr, E.R. / Garman, E.F. / Laver, W.G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2sil.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2sil.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 2sil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/2sil ftp://data.pdbj.org/pub/pdb/validation_reports/si/2sil | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO 136 |
-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) / Gene: PSX62 / Plasmid: PSX62 / References: UniProt: P29768, exo-alpha-sialidase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.62 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | Num. obs: 59728 / % possible obs: 55.9 % / Observed criterion σ(I): 3 |
---|---|
Reflection | *PLUS Highest resolution: 1.6 Å / Num. obs: 35140 / % possible obs: 69.6 % / Redundancy: 1.7 % / Num. measured all: 59728 / Rmerge(I) obs: 0.059 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.6→6 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.163 / Rfactor Rwork: 0.163 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_planar_d / Dev ideal: 0.017 |