+Open data
-Basic information
Entry | Database: PDB / ID: 6ol6 | ||||||
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Title | Structure of iglb12 scFv in complex with anti-idiotype ib2 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / glb12 / Antibody / ib2 / Fab / complex / Anti-Idiotype / HIV / Neutralizing / Broadly | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Weidle, C. / Pancera, M. / Gewe, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Exp.Med. / Year: 2019 Title: Detection and activation of HIV broadly neutralizing antibody precursor B cells using anti-idiotypes. Authors: Bancroft, T. / DeBuysscher, B.L. / Weidle, C. / Schwartz, A. / Wall, A. / Gray, M.D. / Feng, J. / Steach, H.R. / Fitzpatrick, K.S. / Gewe, M.M. / Skog, P.D. / Doyle-Cooper, C. / Ota, T. / ...Authors: Bancroft, T. / DeBuysscher, B.L. / Weidle, C. / Schwartz, A. / Wall, A. / Gray, M.D. / Feng, J. / Steach, H.R. / Fitzpatrick, K.S. / Gewe, M.M. / Skog, P.D. / Doyle-Cooper, C. / Ota, T. / Strong, R.K. / Nemazee, D. / Pancera, M. / Stamatatos, L. / McGuire, A.T. / Taylor, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ol6.cif.gz | 259.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ol6.ent.gz | 209.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ol6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/6ol6 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/6ol6 | HTTPS FTP |
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-Related structure data
Related structure data | 6ol5C 1hzhS 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: 24416.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) |
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#2: Antibody | Mass: 23810.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): hybridoma / Production host: Mus musculus (house mouse) |
#3: Antibody | Mass: 15303.977 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: 12291.675 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 , 2 types, 314 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.95 Å3/Da / Density % sol: 58.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 13.4% PEG 8000, 13.4 PEG 400, 0.1 M MgCl2, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 26000 / % possible obs: 99.5 % / Redundancy: 7.4 % / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.6→2.64 Å / Num. unique obs: 1171 / % possible all: 91.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HZH Resolution: 2.6→49.105 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→49.105 Å
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Refine LS restraints |
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LS refinement shell |
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