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Yorodumi- PDB-6gc2: AbLIFT: Antibody stability and affinity optimization by computati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gc2 | ||||||
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Title | AbLIFT: Antibody stability and affinity optimization by computational design of the variable light-heavy chain interface | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Warszawski, S. / Katz, A. / Khmelnitsky, L. / Ben Nissan, G. / Javitt, G. / Dym, O. / Unger, T. / Knop, O. / Diskin, R. / Albeck, S. ...Warszawski, S. / Katz, A. / Khmelnitsky, L. / Ben Nissan, G. / Javitt, G. / Dym, O. / Unger, T. / Knop, O. / Diskin, R. / Albeck, S. / Fass, D. / Sharon, M. / Fleishman, S.J. | ||||||
Citation | Journal: Plos Comput.Biol. / Year: 2019 Title: Optimizing antibody affinity and stability by the automated design of the variable light-heavy chain interfaces. Authors: Warszawski, S. / Katz, A.B. / Lipsh, R. / Khmelnitsky, L. / Ben Nissan, G. / Javitt, G. / Dym, O. / Unger, T. / Knop, O. / Albeck, S. / Diskin, R. / Fass, D. / Sharon, M. / Fleishman, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gc2.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gc2.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/6gc2 ftp://data.pdbj.org/pub/pdb/validation_reports/gc/6gc2 | HTTPS FTP |
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-Related structure data
Related structure data | 1mlbS 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: 27386.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24356.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Mg formate 2H2O 0.1M Na acetate 3H2O 18% PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5419 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→38.76 Å / Num. obs: 16233 / % possible obs: 99.92 % / Redundancy: 2.6 % / Biso Wilson estimate: 26.15 Å2 / Rmerge(I) obs: 0.08729 / Net I/σ(I): 6.85 |
Reflection shell | Resolution: 2.55→2.641 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.3291 / Mean I/σ(I) obs: 2.01 / Num. unique obs: 1575 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MLB Resolution: 2.55→39.644 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.79 / 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: 2.55→39.644 Å
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Refine LS restraints |
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LS refinement shell |
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