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- PDB-6n7j: BDBV223 Fab bound to synthetic peptide of Bundibugyo virus Glycop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6n7j | |||||||||
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Title | BDBV223 Fab bound to synthetic peptide of Bundibugyo virus Glycoprotein Stalk | |||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / antibody / antiviral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | King, L.B. / West, B.R. / Saphire, E.O. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cross-reactive neutralizing human survivor monoclonal antibody BDBV223 targets the ebolavirus stalk. Authors: King, L.B. / West, B.R. / Moyer, C.L. / Gilchuk, P. / Flyak, A. / Ilinykh, P.A. / Bombardi, R. / Hui, S. / Huang, K. / Bukreyev, A. / Crowe Jr., J.E. / Saphire, E.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.5 KB | Display | ![]() |
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PDB format | ![]() | 264.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 41.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n7uC ![]() 6mamS 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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Unit cell |
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Components
#1: Antibody | Mass: 24582.586 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23817.580 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Protein/peptide | Mass: 1914.183 Da / Num. of mol.: 2 / Fragment: UNP residues 620-635 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 20% w/v PEG8000, 0.2 M magnesium acetate, 0.1 M sodium cacodylate:HCl, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 70 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.68→48.356 Å / Num. obs: 12104 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.19 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 3.68→3.82 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.68 / Num. unique obs: 1176 / CC1/2: 0.79 / Rpim(I) all: 0.43 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 6MAM chains H & L Resolution: 3.684→48.356 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.684→48.356 Å
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Refine LS restraints |
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LS refinement shell |
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