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- PDB-4yz5: Crystal Structure of Streptococcus pneumoniae NanC, in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yz5 | |||||||||
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Title | Crystal Structure of Streptococcus pneumoniae NanC, in complex with 3-Sialyllactose | |||||||||
![]() | Putative neuraminidase | |||||||||
![]() | HYDROLASE / Sialidase / Neuraminidase / Beta-propeller / CBM40 | |||||||||
Function / homology | ![]() 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 / carbohydrate metabolic process / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lukacik, P. / Owen, C.D. / Potter, J.A. / Taylor, G.L. / Walsh, M.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR. Authors: Owen, C.D. / Lukacik, P. / Potter, J.A. / Sleator, O. / Taylor, G.L. / Walsh, M.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.3 KB | Display | ![]() |
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PDB format | ![]() | 227.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 51.8 KB | Display | |
Data in CIF | ![]() | 76.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yw1C ![]() 4yw2C ![]() 4yw3C ![]() 4yw5C ![]() 4yz1C ![]() 4yz2C ![]() 4yz4C ![]() 5f9tC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 84 - 740 / Label seq-ID: 21 - 677
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Components
#1: Protein | Mass: 75996.844 Da / Num. of mol.: 2 / Fragment: Sialidase NanC Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q97Q99, UniProt: A0A0H2UQE4*PLUS, exo-alpha-sialidase #2: Polysaccharide | #3: Sugar | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % / Description: needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG3350, 0.25M Ammonium sulfate, 0.1M Hepes pH8, 7.5% Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 17, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→75.04 Å / Num. obs: 70273 / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.326 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.27→2.33 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.375 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.95 Å2 / Biso mean: 21.429 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.27→75.04 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 83202 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.27→2.329 Å / Total num. of bins used: 20
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