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- PDB-6pzd: Crystal structure of the neuraminidase stabilization mutant Y169a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pzd | |||||||||
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Title | Crystal structure of the neuraminidase stabilization mutant Y169aH from A/Shanghai/2/2013 (H7N9) | |||||||||
![]() | Neuraminidase![]() | |||||||||
![]() | ![]() ![]() | |||||||||
Function / homology | ![]() exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / exo-alpha-(2->3)-sialidase activity / ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhu, X. / Wilson, I.A. | |||||||||
Funding support | ![]()
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Validation Report | ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
-Related structure data
Related structure data | ![]() 6pzeC ![]() 6pzfC ![]() 6pzgC ![]() 6pzhC ![]() 6pzwC ![]() 6pzyC ![]() 6pzzC ![]() 6u02C ![]() 5l14S S: Starting model for refinement C: citing same article ( |
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Similar-shape strucutres |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell | γ α β
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 44014.000 Da / Num. of mol.: 1 / Mutation: Y169H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: A/Shanghai/02/2013(H7N9) / Production host: ![]() ![]() ![]() References: UniProt: V9NZ28, UniProt: R4NFR6*PLUS, exo-alpha-sialidase |
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-Sugars , 2 types, 2 molecules 
#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-(1-2)-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 |
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#5: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 4 types, 600 molecules 






#3: Chemical | ChemComp-EDO / ![]() #4: Chemical | ChemComp-MES / | ![]() #6: Chemical | ChemComp-CA / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.05 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 12% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.12→43 Å / Num. obs: 194141 / % possible obs: 99.9 % / Redundancy: 22.3 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.1 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.12→1.13 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6246 / CC1/2: 0.834 / Rpim(I) all: 0.45 / Rsym value: 0.92 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5L14 Resolution: 1.12→42.949 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→42.949 Å
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Refine LS restraints |
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LS refinement shell |
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