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Open data
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Basic information
Entry | Database: PDB / ID: 7paa | ||||||
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Title | JC polyomavirus VP1 in complex with scFv 29B1 | ||||||
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![]() | VIRAL PROTEIN / antibody / polyomavirus / VP1 / neutralization | ||||||
Function / homology | ![]() T=7 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harprecht, C. / Stroeh, L.J. / Freytag, J. / Stehle, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of human neutralizing antibodies against JC and BK polyomavirus Authors: Harprecht, C. / Stroeh, L.J. / Senn, L. / O'Hara, B.A. / Nagel, F. / Freytag, J. / Stiehrof, Y.D. / Atwood, W.J. / Combaluzier, B. / Stehle, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 928.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 539.7 KB | Display | ![]() |
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Full document | ![]() | 559.4 KB | Display | |
Data in XML | ![]() | 151.8 KB | Display | |
Data in CIF | ![]() | 202.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pa6C ![]() 7pa7C ![]() 7pa8C ![]() 7pa9C ![]() 3nxgS ![]() 4kq3S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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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Unit cell |
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Components
#1: Antibody | Mass: 26947.736 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 30075.861 Da / Num. of mol.: 10 / Fragment: UNP residues 23-290 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M trimethanolamine N-oxide, 0.1 M Tris (pH 8.5), 20% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.5 Å / Num. obs: 129715 / % possible obs: 99.8 % / Redundancy: 7.06 % / CC1/2: 0.99 / Rrim(I) all: 0.23 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 3→3.18 Å / Mean I/σ(I) obs: 2.21 / Num. unique obs: 20801 / CC1/2: 0.72 / Rrim(I) all: 0.95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NXG, 4KQ3 Resolution: 3.102→48.507 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.195 / Average fsc free: 0.9053 / Average fsc work: 0.9098 / Cross valid method: FREE R-VALUE / ESU R Free: 0.441 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.614 Å2
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Refinement step | Cycle: LAST / Resolution: 3.102→48.507 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: 20
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