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Yorodumi- PDB-5xhv: Crystal Structure Of Fab S40 In Complex With Influenza Hemaggluti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xhv | ||||||
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Title | Crystal Structure Of Fab S40 In Complex With Influenza Hemagglutinin, HA1 subunit. | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM 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 / 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 | Influenza A virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Lee, C.C. / Wang, A.H.J. / Yu, C.M. / Yang, A.S. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: High throughput discovery of influenza virus neutralizing antibodies from phage-displayed synthetic antibody libraries. Authors: Chen, I.C. / Chiu, Y.K. / Yu, C.M. / Lee, C.C. / Tung, C.P. / Tsou, Y.L. / Huang, Y.J. / Lin, C.L. / Chen, H.S. / Wang, A.H. / Yang, A.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xhv.cif.gz | 287.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xhv.ent.gz | 232.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/5xhv ftp://data.pdbj.org/pub/pdb/validation_reports/xh/5xhv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35986.641 Da / Num. of mol.: 2 / Fragment: HA1 subunit (UNP RESIDUES 18-341) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1)) Strain: A/California/07/2009(H1N1) / Gene: HA Production host: Insect cell expression vector pTIE1 (others) References: UniProt: C3W5X2 #2: Antibody | Mass: 24445.262 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23618.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293 / Production host: Homo sapiens (human) |
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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: 4.97 Å3/Da / Density % sol: 75.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 8%(w/v) PEG 6000, 1N NaOH, 15% MPD, 0.1 M Na HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 94 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→25 Å / Num. obs: 34636 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 3.35→3.47 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W9D, 3HC4, 3GBN Resolution: 3.35→25 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.899 / SU B: 26.695 / SU ML: 0.429 / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 173.528 Å2
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Refinement step | Cycle: 1 / Resolution: 3.35→25 Å
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Refine LS restraints |
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