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Yorodumi- PDB-7aey: Salmonella typhimurium neuraminidase in complex with isocarba-DANA. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aey | ||||||
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Title | Salmonella typhimurium neuraminidase in complex with isocarba-DANA. | ||||||
Components | Sialidase | ||||||
Keywords | HYDROLASE / Salmonella typhimurium / enzyme / complex / isocarba-DANA / neuraminidase / sialidase / carbocyclic DANA analogue / DANA | ||||||
Function / homology | Function and homology information exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / : / : / : / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.919 Å | ||||||
Authors | Salinger, M.T. / Kuhn, P. / Laver, W.G. / Pape, T. / Schneider, T.R. / Sheldrick, G.M. / Vasella, A.T. / Vimr, E.R. / Vorwerk, S. / Garman, E.F. | ||||||
Citation | Journal: To Be Published Title: Salmonella typhimurium neuraminidase in complex with isocarba-DANA. Authors: Garman, E.F. / Salinger, M.T. / Laver, W.G. / Kuhn, P. / Pape, T. / Schneider, T.R. / Sheldrick, G.M. / Vasella, A.T. / Vimr, E.R. / Vorwerk, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7aey.cif.gz | 334.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aey.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7aey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7aey_validation.pdf.gz | 796.5 KB | Display | wwPDB validaton report |
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Full document | 7aey_full_validation.pdf.gz | 805.7 KB | Display | |
Data in XML | 7aey_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 7aey_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/7aey ftp://data.pdbj.org/pub/pdb/validation_reports/ae/7aey | HTTPS FTP |
-Related structure data
Related structure data | 3silS S: Starting model for refinement |
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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: 41791.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: isocarba-DANA: isocarba-2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: nanH, STM0928 / Production host: Escherichia coli (E. coli) / References: UniProt: P29768, exo-alpha-sialidase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-R8T / ( | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then ...Details: Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes. A 2.5mM solution of isocarba-DANA was then soaked into the resultant crystals for 90 minutes at a temperature of 293K. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.79 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 27, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.79 Å / Relative weight: 1 |
Reflection | Resolution: 0.918→24.325 Å / Num. obs: 236859 / % possible obs: 97.8 % / Redundancy: 3.5 % / Rrim(I) all: 0.078 / Rsym value: 0.07 / Net I/σ(I): 19.78 |
Reflection shell | Resolution: 0.92→0.94 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 28378 / Rrim(I) all: 0.511 / Rsym value: 0.393 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SIL Resolution: 0.919→24.321 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.983 / WRfactor Rfree: 0.113 / WRfactor Rwork: 0.097 / SU B: 0.389 / SU ML: 0.01 / Average fsc free: 0.9632 / Average fsc work: 0.9661 / Cross valid method: FREE R-VALUE / ESU R: 0.014 / ESU R Free: 0.015 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.866 Å2
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Refinement step | Cycle: LAST / Resolution: 0.919→24.321 Å
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Refine LS restraints |
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LS refinement shell |
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