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- PDB-6oz2: Crystal structure of the broadly neutralizing antibody N49P6 Fab ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6oz2 | ||||||||||||
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Title | Crystal structure of the broadly neutralizing antibody N49P6 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core. | ||||||||||||
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![]() | IMMUNE SYSTEM / HIV-1 / VRC01-CLASS ANTIBODY / CD4 BINDING SITE / CLADE A/E 93TH057 GP120 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / N49P6 | ||||||||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / viral envelope / clade A/E 93TH057 HIV-1 gp120 core![]() | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Tolbert, W.D. / Pazgier, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Near-Pan-neutralizing, Plasma Deconvoluted Antibody N49P6 Mimics Host Receptor CD4 in Its Quaternary Interactions with the HIV-1 Envelope Trimer. Authors: Tolbert, W.D. / Nguyen, D.N. / Tehrani, Z.R. / Sajadi, M.M. / Pazgier, M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.6 KB | Display | ![]() |
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PDB format | ![]() | 256.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.1 KB | Display | ![]() |
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Full document | ![]() | 494.3 KB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 42.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6oz4C ![]() 6bckS 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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Unit cell |
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Components
#1: Protein | Mass: 39356.613 Da / Num. of mol.: 1 / Mutation: H375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Antibody | Mass: 24885.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#3: Antibody | Mass: 21810.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
#4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG 3350 0.1 M Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2017 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→50 Å / Num. obs: 31853 / % possible obs: 92 % / Redundancy: 3.1 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.166 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.55→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.727 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1524 / CC1/2: 0.56 / Rpim(I) all: 0.556 / % possible all: 89.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BCK Resolution: 2.55→34.327 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→34.327 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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