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Yorodumi- PDB-4eef: Crystal structure of the designed inhibitor protein F-HB80.4 in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eef | |||||||||
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Title | Crystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918 influenza virus hemagglutinin. | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/INHIBITOR / immunoglobulin / hemagglutinin / Fusion of virus membrane with host membrane / membrane fusion / Sialic acid / Virion / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR complex | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus Artificial Gene (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å | |||||||||
Authors | Dreyfus, C. / Wilson, I.A. | |||||||||
Citation | Journal: Nat.Biotechnol. / Year: 2012 Title: Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Authors: Whitehead, T.A. / Chevalier, A. / Song, Y. / Dreyfus, C. / Fleishman, S.J. / De Mattos, C. / Myers, C.A. / Kamisetty, H. / Blair, P. / Wilson, I.A. / Baker, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eef.cif.gz | 324.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eef.ent.gz | 266.8 KB | Display | PDB format |
PDBx/mmJSON format | 4eef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4eef_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4eef_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4eef_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 4eef_validation.cif.gz | 83.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/4eef ftp://data.pdbj.org/pub/pdb/validation_reports/ee/4eef | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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: 36452.797 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/SOUTH CAROLINA/1/1918 (H1N1) / Gene: HA, hemagglutinin / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HIGH FIVE / References: UniProt: Q9WFX3 #2: Protein | Mass: 20394.445 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/SOUTH CAROLINA/1/1918 (H1N1) / Gene: HA, hemagglutinin / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HIGH FIVE / References: UniProt: Q9WFX3 #3: Protein | Mass: 8810.759 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Artificial Gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (BL21/DE3) #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 16% PEG3350, and 100mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 70 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03326 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03326 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 58197 / Num. obs: 58197 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.704→43.673 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 29.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.165 Å2 / ksol: 0.294 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.704→43.673 Å
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Refine LS restraints |
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LS refinement shell |
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