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- PDB-6ofi: CRYSTAL STRUCTURE OF the RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB I... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ofi | ||||||||||||
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Title | CRYSTAL STRUCTURE OF the RV144 C1-C2 SPECIFIC ANTIBODY CH55 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 | ||||||||||||
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![]() | IMMUNE SYSTEM / ANTI-HIV-1 ENV ANTIBODY CH55 / CD4I ANTIBODY / ADCC / HIV-1 ENV / RV144 VACCINE TRIAL / CLADE A/E 93TH057 / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX | ||||||||||||
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. / Yan, F. / Van, V. / 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 | ![]() | 309.1 KB | Display | ![]() |
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PDB format | ![]() | 252 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.7 KB | Display | ![]() |
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Full document | ![]() | 507.4 KB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 41.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fz8C ![]() 6mg7C ![]() 6oedSC ![]() 6oejC ![]() 3tgtS 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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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: 24004.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23444.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.97 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 15% PEG 6000, 0.1 M sodium citrate pH 5.5 |
-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: May 28, 2018 |
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: 3.85→50 Å / Num. obs: 8672 / % possible obs: 81.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 3.85→3.92 Å / Redundancy: 3.3 % / Num. unique obs: 448 / CC1/2: 0.449 / Rpim(I) all: 0.567 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OED, 3TGT Resolution: 3.85→41.43 Å / SU ML: 0.74 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.85→41.43 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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