[English] 日本語
![](img/lk-miru.gif)
- PDB-4k3y: Crystal structure of a subtype N11 neuraminidase-like protein of ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4k3y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a subtype N11 neuraminidase-like protein of A/flat-faced bat/Peru/033/2010 (H18N11) | |||||||||
![]() | neuraminidase | |||||||||
![]() | VIRAL PROTEIN / influenza virus / neuraminidase-like / N11 / beta propeller | |||||||||
Function / homology | Neuraminidase - #10 / 6 Propeller / Neuraminidase / Mainly Beta![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhu, X. / Wilson, I.A. | |||||||||
![]() | ![]() Title: New world bats harbor diverse influenza a viruses. Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / ...Authors: Tong, S. / Zhu, X. / Li, Y. / Shi, M. / Zhang, J. / Bourgeois, M. / Yang, H. / Chen, X. / Recuenco, S. / Gomez, J. / Chen, L.M. / Johnson, A. / Tao, Y. / Dreyfus, C. / Yu, W. / McBride, R. / Carney, P.J. / Gilbert, A.T. / Chang, J. / Guo, Z. / Davis, C.T. / Paulson, J.C. / Stevens, J. / Rupprecht, C.E. / Holmes, E.C. / Wilson, I.A. / Donis, R.O. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 569.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 473 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4k3xC ![]() 4mc5C ![]() 4mc7C ![]() 4gdiS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40294.918 Da / Num. of mol.: 4 / Fragment: ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Sugars , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 2 types, 121 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.4 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8 Details: 0.2 M potassium sulfate, 18% PEG3350, pH 8.0, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2012 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→50 Å / Num. obs: 70321 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Rsym value: 0.08 |
Reflection shell | Resolution: 2.68→2.73 Å / % possible all: 99.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4GDI Resolution: 2.682→48.87 Å / SU ML: 0.93 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.06 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.547 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.682→48.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 98.3731 Å / Origin y: -15.8911 Å / Origin z: 23.1232 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |