+Open data
-Basic information
Entry | Database: PDB / ID: 6ytb | ||||||
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Title | GLYCOSYLATED KNOB/DUMMY-HOLE/DUMMY FC FRAGMENT | ||||||
Components | (Immunoglobulin gamma-1 heavy chain) x 2 | ||||||
Keywords | IMMUNE SYSTEM / BISPECIFIC ANTIBODY FC ENGINEERING / KNOB-INTO-HOLE / FORMAT CHAIN EXCHANGE / FORCE | ||||||
Function / homology | Function and homology information immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Kuglstatter, A. / Leibrock, L. / Benz, J. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Format chain exchange (FORCE) for high-throughput generation of bispecific antibodies in combinatorial binder-format matrices. Authors: Dengl, S. / Mayer, K. / Bormann, F. / Duerr, H. / Hoffmann, E. / Nussbaum, B. / Tischler, M. / Wagner, M. / Kuglstatter, A. / Leibrock, L. / Buldun, C. / Georges, G. / Brinkmann, U. #1: Journal: To Be Published Title: Format Chain Exchange (FORCE) - a robust high throughput approach for combinatorial generation of bispecific antibodies in different formats Authors: Dengl, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ytb.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ytb.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ytb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/6ytb ftp://data.pdbj.org/pub/pdb/validation_reports/yt/6ytb | HTTPS FTP |
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-Related structure data
Related structure data | 6yscC 6yt7C 5hy9S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Antibody | Mass: 27086.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 | ||||
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#2: Antibody | Mass: 26881.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HOLE-DUMMY PROTEIN (E357K,T366S,L368A,Y407V) / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5 | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.2M potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→74.85 Å / Num. obs: 61292 / % possible obs: 95.1 % / Redundancy: 6.6 % / CC1/2: 1 / Rpim(I) all: 0.024 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.65→1.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3069 / CC1/2: 0.57 / Rpim(I) all: 0.568 / % possible all: 51.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HY9 Resolution: 1.65→46.7 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.66 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.56 Å2 / Biso mean: 38.2323 Å2 / Biso min: 15.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→46.7 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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