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Open data
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Basic information
Entry | Database: PDB / ID: 4xyx | ||||||
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Title | NanB plus Optactamide | ||||||
![]() | Sialidase B | ||||||
![]() | HYDROLASE / Inhibitor binding | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Rogers, G.W. / Brear, P. / Yang, L. / Taylor, G.L. / Westwood, N.J. | ||||||
![]() | ![]() Title: The Hunt for Serendipitous Allosteric Sites: Discovery of a novel allosteric inhibitor of the bacterial sialidase NanB Authors: Brear, P. / Rogers, G.W. / Yang, L. / Chen, A.S. / Mitchell, J.B.O. / Taylor, G.L. / Westwood, N.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 155.9 KB | Display | ![]() |
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PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 751.2 KB | Display | ![]() |
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Full document | ![]() | 758.5 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 41.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xe9C ![]() 4xhbC ![]() 4xhxC ![]() 4xjzC ![]() 4xmiC ![]() 4xogC ![]() 2vw2S 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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Unit cell |
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Components
#1: Protein | Mass: 73778.141 Da / Num. of mol.: 1 / Fragment: UNP residues 40-697 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-43Z / | ||
#3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100mM Imidazole pH8, 5% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 12, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 42642 / % possible obs: 98.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.071 / Χ2: 2.902 / Net I/av σ(I): 38.04 / Net I/σ(I): 18.4 / Num. measured all: 234475 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VW2 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.2161 / WRfactor Rwork: 0.1706 / FOM work R set: 0.8358 / SU B: 4.201 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2233 / SU Rfree: 0.1869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.36 Å2 / Biso mean: 24.982 Å2 / Biso min: 10.61 Å2
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Refinement step | Cycle: final / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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