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- PDB-3uyw: Crystal structures of globular head of 2009 pandemic H1N1 hemaggl... -
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Basic information
Entry | Database: PDB / ID: 3uyw | ||||||
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Title | Crystal structures of globular head of 2009 pandemic H1N1 hemagglutinin | ||||||
![]() | Hemagglutinin | ||||||
![]() | VIRAL PROTEIN / Influenza virus / subunit vaccine / hemagglutinin (HA) | ||||||
Function / homology | ![]() viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xuan, C.L. / Shi, Y. / Qi, J.X. / Xiao, H.X. / Gao, G.F. | ||||||
![]() | ![]() Title: Structural vaccinology: structure-based design of influenza A virus hemagglutinin subtype-specific subunit vaccines Authors: Xuan, C.L. / Shi, Y. / Qi, J.X. / Zhang, W. / Xiao, H.X. / 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 | ![]() | 354.7 KB | Display | ![]() |
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PDB format | ![]() | 288.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.9 KB | Display | ![]() |
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Full document | ![]() | 497.3 KB | Display | |
Data in XML | ![]() | 44.6 KB | Display | |
Data in CIF | ![]() | 63.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3uyxC ![]() 3al4S 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24137.064 Da / Num. of mol.: 4 / Fragment: UNP residues 65-278 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% PEG 6000, 5% MPD, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 26, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 59386 / Num. obs: 59386 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 95.4 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3AL4 Resolution: 1.903→35.134 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8704 / SU ML: 0.24 / σ(F): 0.08 / Phase error: 20.65 / 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 / Bsol: 40.099 Å2 / ksol: 0.361 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.55 Å2 / Biso mean: 27.8911 Å2 / Biso min: 7.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.903→35.134 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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Refinement TLS params. | Method: refined / Origin x: 8.5222 Å / Origin y: -17.6252 Å / Origin z: 32.2131 Å
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Refinement TLS group | Selection details: all |