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Open data
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Basic information
Entry | Database: PDB / ID: 7pa7 | ||||||
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Title | BK polyomavirus VP1 in complex with scFv 29B1 | ||||||
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![]() | VIRAL PROTEIN / antibody / polyomavirus / VP1 / neutralization | ||||||
Function / homology | ![]() caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / 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 | ![]() | 923.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7pa6C ![]() 7pa8C ![]() 7pa9C ![]() 7paaC ![]() 4kq3S ![]() 4mj1S 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: 30261.039 Da / Num. of mol.: 10 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: 3.05 Å3/Da / Density % sol: 59.65 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium malonate (pH 5.5), 14.4% PEG 3350 |
-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 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49.2 Å / Num. obs: 181005 / % possible obs: 94.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 34 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.17 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.6→2.81 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 55527 / CC1/2: 0.61 / Rrim(I) all: 0.74 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MJ1, 4KQ3 Resolution: 2.6→48.444 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.223 / Average fsc free: 0.8545 / Average fsc work: 0.865 / Cross valid method: FREE R-VALUE / ESU R: 0.764 / ESU R Free: 0.335 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: 26.747 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→48.444 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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