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- PDB-4yw5: Crystal Structure of Streptococcus pneumoniae NanC, complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yw5 | |||||||||
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Title | Crystal Structure of Streptococcus pneumoniae NanC, complex with oseltamivir carboxylate | |||||||||
![]() | Neuraminidase C | |||||||||
![]() | HYDROLASE / Sialidase / Neuraminidase / oseltamivir / 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 / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Owen, C.D. / Lukacik, P. / Potter, J.A. / Walsh, M. / Taylor, G.L. | |||||||||
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 | ![]() | 529.6 KB | Display | ![]() |
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PDB format | ![]() | 435.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 868.8 KB | Display | ![]() |
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Full document | ![]() | 874.1 KB | Display | |
Data in XML | ![]() | 48.6 KB | Display | |
Data in CIF | ![]() | 68.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yw1C ![]() 4yw2C ![]() 4yw3C ![]() 4yz1C ![]() 4yz2C ![]() 4yz4C ![]() 4yz5C ![]() 5f9tC ![]() 2vw0S S: Starting model for refinement 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: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 83 - 741 / Label seq-ID: 1 - 659
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Components
#1: Protein | Mass: 73978.609 Da / Num. of mol.: 2 / Fragment: unp residues 83-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-334 / TIGR4 / Gene: SP_1326,nanC / Plasmid: pET21b / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 16% PEG8000, 20% glycerol, 40mM monopotassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 23, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→40 Å / Num. obs: 71545 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.089 / Χ2: 1.973 / Net I/av σ(I): 14.779 / Net I/σ(I): 10.1 / Num. measured all: 221378 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2vw0 Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2026 / WRfactor Rwork: 0.1777 / FOM work R set: 0.7879 / SU B: 15.409 / SU ML: 0.18 / SU R Cruickshank DPI: 0.3268 / SU Rfree: 0.2252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.79 Å2 / Biso mean: 40.614 Å2 / Biso min: 12.16 Å2
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Refinement step | Cycle: final / Resolution: 2.3→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 83088 / 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: 2.3→2.359 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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