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- PDB-4cyz: Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutini... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cyz | |||||||||
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Title | Structure of the A_mallard_Sweden_51_2002 H10 Avian Haemmaglutinin in complex with avian receptor analog LSTA | |||||||||
![]() | (HEMAGGLUTININ![]() | |||||||||
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Function / homology | ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Haire, L.F. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J. | |||||||||
![]() | ![]() Title: Receptor Binding by H10 Influenza Viruses. Authors: Vachieri, S.G. / Xiong, X. / Collins, P.J. / Walker, P.A. / Martin, S.R. / Haire, L.F. / Zhang, Y. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.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 | ![]() | 598.4 KB | Display | ![]() |
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PDB format | ![]() | 496.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cyvSC ![]() 4cywC ![]() 4cz0C ![]() 4d00C 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
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | ![]() Mass: 34651.934 Da / Num. of mol.: 3 / Fragment: HA1, RESIDUES 18-335 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: E0YNJ7 #2: Protein | ![]() Mass: 19774.662 Da / Num. of mol.: 3 / Fragment: HA2, RESIDUES 341-513 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: E0YNJ7 |
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-Sugars , 6 types, 12 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||||||
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#4: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #5: 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 #6: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose | ![]() Source method: isolated from a genetically manipulated source #7: 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 #8: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 2 types, 432 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#9: Chemical | ChemComp-EDO / ![]() #10: 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: 59.12 % / Description: NONE |
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Crystal grow![]() | Details: 18 PERCENT PEG 2000MME AND 0.1 M BICINE PH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→62.86 Å / Num. obs: 75050 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 4 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4CYV Resolution: 2.4→115.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 17.814 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 47.615 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→115.29 Å
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Refine LS restraints |
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