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- PDB-6mg7: Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mg7 | ||||||||||||
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Title | Crystal structure of the RV144 C1-C2 specific antibody CH54 Fab in complex with HIV-1 CLADE A/E GP120 and M48U1 | ||||||||||||
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Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Van, V. / Tolbert, W.D. / Pazgier, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Recognition Patterns of the C1/C2 Epitopes Involved in Fc-Mediated Response in HIV-1 Natural Infection and the RV114 Vaccine Trial. Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. ...Authors: Tolbert, W.D. / Van, V. / Sherburn, R. / Tuyishime, M. / Yan, F. / Nguyen, D.N. / Stanfield-Oakley, S. / Easterhoff, D. / Bonsignori, M. / Haynes, B.F. / Moody, M.A. / Ray, K. / Ferrari, G. / Lewis, G.K. / 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 | ![]() | 318.1 KB | Display | ![]() |
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PDB format | ![]() | 257.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4fz8C ![]() 6oedC ![]() 6oejC ![]() 6ofiC ![]() 4rfoS 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: 42847.676 Da / Num. of mol.: 1 / Mutation: H375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Protein/peptide | | ||
#3: Antibody | Mass: 23532.475 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Antibody | Mass: 22637.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#5: Sugar | ChemComp-NAG / ![]() Compound details | THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 4000 0.1 M MES pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2018 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.9→50 Å / Num. obs: 16963 / % possible obs: 95.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.174 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4RFO Resolution: 2.91→39.68 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.872 / SU B: 85.574 / SU ML: 0.71 / Cross valid method: THROUGHOUT / ESU R Free: 0.571 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→39.68 Å
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Refine LS restraints |
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