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- PDB-6crd: INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6crd | |||||||||
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Title | INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk | |||||||||
![]() | Tetrabrachion,Neuraminidase | |||||||||
![]() | viral protein/hydrolase / NEURAMINIDASE / SIALIDASE / HYDROLASE(O-GLUCOSYL) / HYDROLASE-HYDROLASE / ARTIFICIAL STALK / Tetrabrachion / HYDROLASE / viral protein-hydrolase complex | |||||||||
Function / homology | ![]() exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Streltsov, V.A. / Schmidt, P. / McKimm-Breschkin, J. | |||||||||
![]() | ![]() Title: Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk. Authors: Streltsov, V.A. / Schmidt, P.M. / McKimm-Breschkin, J.L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 726.9 KB | Display | ![]() |
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PDB format | ![]() | 607.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.1 MB | Display | ![]() |
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Full document | ![]() | 7.3 MB | Display | |
Data in XML | ![]() | 155.5 KB | Display | |
Data in CIF | ![]() | 212.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d3bC ![]() 6mcxC ![]() 7nn9S 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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2 | ![]()
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Unit cell |
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Components
-Protein / Non-polymers , 2 types, 941 molecules ABCDEFGH![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 53448.930 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pMA (ampR) / Strain: A/Tern/Australia/G70C/1975 H11N9 / Gene: NA / Cell line (production host): S. frugiperda (SF9) Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q54436, UniProt: P03472, exo-alpha-sialidase #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 31 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose 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)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES buffer at pH7.0 with 10% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2011 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.57→40.04 Å / Num. obs: 108611 / % possible obs: 77.6 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.307 / Net I/σ(I): 2.7 | |||||||||||||||
Reflection shell | Resolution: 2.57→2.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1 / Num. unique obs: 2590 / % possible all: 70.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7NN9 Resolution: 2.57→40.04 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.749 / SU B: 7.915 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.509 Å2
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Refinement step | Cycle: 1 / Resolution: 2.57→40.04 Å
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Refine LS restraints |
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