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- PDB-4gdi: A subtype N10 neuraminidase-like protein of A/little yellow-shoul... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gdi | |||||||||
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Title | A subtype N10 neuraminidase-like protein of A/little yellow-shouldered bat/Guatemala/164/2009 | |||||||||
![]() | Neuraminidase | |||||||||
![]() | VIRAL PROTEIN / INFLUENZA VIRUS / NEURAMINIDASE-LIKE / N10 / BETA-PROPELLER / ECTODOMAIN | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / identical protein binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhu, X. / Wilson, I.A. | |||||||||
![]() | ![]() Title: Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site. Authors: Zhu, X. / Yang, H. / Guo, Z. / Yu, W. / Carney, P.J. / Li, Y. / Chen, L.M. / Paulson, J.C. / Donis, R.O. / Tong, S. / Stevens, J. / Wilson, I.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 | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 94.6 KB | Display | |
Data in CIF | ![]() | 135.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gdjC ![]() 4gezC ![]() 3beqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 41590.883 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: A/little yellow-shouldered bat/Guatemala/164/2009(H17N10)) Gene: NA / Plasmid: pFastbacHT-A / Production host: ![]() |
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-Sugars , 7 types, 21 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
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#3: 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)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...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 #6: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 1447 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
#9: Chemical | ChemComp-CA / #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-NO3 / #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Mg nitrate, 14% polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2011 |
Radiation | Monochromator: SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 210731 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 41.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.889 / % possible all: 99.5 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.2_869) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BEQ Resolution: 1.95→40.11 Å / SU ML: 0.62 / σ(F): 1.34 / Phase error: 24.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.13 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.95→40.11 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 18.7921 Å / Origin y: 52.5581 Å / Origin z: 54.0801 Å
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Refinement TLS group | Selection details: ALL |