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- PDB-6vrq: Crystal structure of gl12A21 Fab in complex with anti-idiotypic i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vrq | ||||||
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Title | Crystal structure of gl12A21 Fab in complex with anti-idiotypic iv12 Fab | ||||||
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![]() | IMMUNE SYSTEM / Fab / Complex / gl12A21 / HIV / CD4-binding site / iv12 | ||||||
Function / homology | : / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aljedani, S.S. / Weidle, C. / Pancera, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies. Authors: Seydoux, E. / Wan, Y.H. / Feng, J. / Wall, A. / Aljedani, S. / Homad, L.J. / MacCamy, A.J. / Weidle, C. / Gray, M.D. / Brumage, L. / Taylor, J.J. / Pancera, M. / Stamatatos, L. / McGuire, A.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 344.3 KB | Display | ![]() |
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PDB format | ![]() | 258.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 273.6 KB | Display | ![]() |
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Full document | ![]() | 273.5 KB | Display | |
Data in XML | ![]() | 1.6 KB | Display | |
Data in CIF | ![]() | 11.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xocC ![]() 7jlkC ![]() 7jlnC ![]() 6mftS 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
-Antibody , 4 types, 4 molecules HLAB
#1: Antibody | Mass: 24004.986 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 23410.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 25232.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Antibody | Mass: 22920.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 5 types, 350 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-K / #8: Chemical | ChemComp-CL / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M KCl 0.1M Tris pH 8 15%w/v PEG MME 2K |
-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: Oct 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→36.12 Å / Num. obs: 34290 / % possible obs: 99.7 % / Redundancy: 2.66 % / Biso Wilson estimate: 41.75 Å2 / CC1/2: 0.997 / Net I/σ(I): 21.98 |
Reflection shell | Resolution: 2.574→2.66 Å / Num. unique obs: 2332 / CC1/2: 0.638 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6mft Resolution: 2.57→36.12 Å / SU ML: 0.3395 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3264 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→36.12 Å
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Refine LS restraints |
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LS refinement shell |
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