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Yorodumi- PDB-6xoc: Crystal structure of glVRC01 Fab in complex with anti-idiotypic i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xoc | ||||||
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Title | Crystal structure of glVRC01 Fab in complex with anti-idiotypic iv4 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / Complex / HIV / CD4-binding site | ||||||
Function / homology | : / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Aljedani, S.S. / Weidle, C. / Pancera, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Cell Rep / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xoc.cif.gz | 189.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xoc.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xoc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/6xoc ftp://data.pdbj.org/pub/pdb/validation_reports/xo/6xoc | HTTPS FTP |
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-Related structure data
Related structure data | 6vrqC 7jlkC 7jlnC 6mftS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 4 types, 4 molecules ABHL
#1: Antibody | Mass: 23983.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23897.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 23841.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 22730.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Non-polymers , 6 types, 247 molecules
#5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | ChemComp-SCN / | #9: Chemical | ChemComp-TRS / | #10: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 7.5, 8%w/v PEG 20K, 8%w/v PEG MME 550 and 0.2 M KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→110.5 Å / Num. obs: 46804 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 36.33 Å2 / CC1/2: 0.99 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.45→2.54 Å / Num. unique obs: 46727 / CC1/2: 0.785 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MFT Resolution: 2.45→50.01 Å / SU ML: 0.274 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8672 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: 45.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→50.01 Å
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Refine LS restraints |
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LS refinement shell |
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