+Open data
-Basic information
Entry | Database: PDB / ID: 1kit | ||||||
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Title | VIBRIO CHOLERAE NEURAMINIDASE | ||||||
Components | SIALIDASENeuraminidase | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / CALCIUM | ||||||
Function / homology | Function and homology information sialic acid binding / 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 / metabolic process / intracellular membrane-bounded organelle ...sialic acid binding / 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 / metabolic process / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Taylor, G.L. / Crennell, S.J. / Garman, E.F. / Vimr, E.R. / Laver, W.G. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Crystal structure of Vibrio cholerae neuraminidase reveals dual lectin-like domains in addition to the catalytic domain. Authors: Crennell, S. / Garman, E. / Laver, G. / Vimr, E. / Taylor, G. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kit.cif.gz | 174.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kit.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 1kit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/1kit ftp://data.pdbj.org/pub/pdb/validation_reports/ki/1kit | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 83039.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: CLASSICAL OGAWA 395 / Gene: NANH / Plasmid: PCVD364 / Gene (production host): NANH / Production host: Escherichia coli (E. coli) References: UniProt: P37060, UniProt: P0C6E9*PLUS, exo-alpha-sialidase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56 % | ||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 40491 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 9.15 % / Rmerge(I) obs: 0.098 |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. measured all: 370535 |
-Processing
Software |
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Refinement | Resolution: 2.3→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.012 / Weight: 5 |