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- PDB-5e5w: Hemagglutinin-esterase-fusion mutant structure of influenza D virus -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e5w | |||||||||
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Title | Hemagglutinin-esterase-fusion mutant structure of influenza D virus | |||||||||
![]() | (Hemagglutinin- ...) x 2 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Song, H. / Qi, J. / Shi, Y. / Gao, G.F. | |||||||||
![]() | ![]() Title: An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism Authors: Song, H. / Qi, J. / Khedri, Z. / Diaz, S. / Yu, H. / Chen, X. / Varki, A. / Shi, Y. / Gao, G.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 471.5 KB | Display | ![]() |
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PDB format | ![]() | 388.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5e62C ![]() 5e64C ![]() 5e65C ![]() 5e66C ![]() 1flcS 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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Unit cell |
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Components
-Hemagglutinin- ... , 2 types, 4 molecules ACBD
#1: Protein | ![]() Mass: 46456.988 Da / Num. of mol.: 2 / Fragment: UNP residues 19-445 / Mutation: S57A, D356A, H359A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: D/swine/Oklahoma/1334/2011 / Gene: HEF / Plasmid: PFASTBAC1 / Cell line (production host): HI5 / Production host: ![]() ![]() #2: Protein | ![]() Mass: 16670.598 Da / Num. of mol.: 2 / Fragment: UNP residues 456-612 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: D/swine/Oklahoma/1334/2011 / Gene: HEF / Production host: ![]() |
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-Sugars , 4 types, 10 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ![]() #6: Sugar | ![]() |
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-Non-polymers , 1 types, 544 molecules ![](data/chem/img/HOH.gif)
#7: Water | ChemComp-HOH / ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.01 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M PCTP (Propionic acid, Cacodylate, Bis-tris propane system) buffer pH 8.5, 22.5%(w/v) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.4→49.55 Å / Num. obs: 57383 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 2.6 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.769 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.769 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1FLC Resolution: 2.4→49.55 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→49.55 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: -7.0205 Å / Origin y: -2.1715 Å / Origin z: -42.6502 Å
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Refinement TLS group | Selection details: ALL |