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Open data
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Basic information
Entry | Database: PDB / ID: 4gay | ||||||
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Title | Structure of the broadly neutralizing antibody AP33 | ||||||
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![]() | IMMUNE SYSTEM / antibody Fab / neutralizing antibody / HCV E2 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / TRIETHYLENE GLYCOL![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Potter, J.A. / Owsianka, A. / Jeffery, N. / Matthews, D. / Keck, Z. / Lau, P. / Foung, S.K.H. / Taylor, G.L. / Patel, A.H. | ||||||
![]() | ![]() Title: Toward a Hepatitis C Virus Vaccine: the Structural Basis of Hepatitis C Virus Neutralization by AP33, a Broadly Neutralizing Antibody. Authors: Potter, J.A. / Owsianka, A.M. / Jeffery, N. / Matthews, D.J. / Keck, Z.Y. / Lau, P. / Foung, S.K. / Taylor, G.L. / Patel, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.5 KB | Display | ![]() |
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PDB format | ![]() | 138.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.7 KB | Display | ![]() |
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Full document | ![]() | 488.4 KB | Display | |
Data in XML | ![]() | 31.5 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | The asymmetric unit contains two biological units |
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Components
#1: Antibody | Mass: 23677.420 Da / Num. of mol.: 2 / Fragment: Fab fragment of AP33 heavy chain / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Antibody | Mass: 23921.352 Da / Num. of mol.: 2 / Fragment: Fab fragment of AP33 light chain / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 18% PEG 8K, 0.1M TrisHCl, 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 9, 2010 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. all: 29053 / Num. obs: 29053 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.65→2.8 Å / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.754 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→24.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.708 Å / Total num. of bins used: 20
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