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Yorodumi- PDB-3vfg: Crystal structure of monoclonal antibody 3F8 Fab fragment that bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vfg | ||||||
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Title | Crystal structure of monoclonal antibody 3F8 Fab fragment that binds to GD2 ganglioside | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / antibody / GD2 Ganglioside | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ahmed, M. / Goldgur, Y. / Cheung, N.-K. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: In silico Driven Redesign of a Clinically Relevant Antibody for the Treatment of GD2 Positive Tumors. Authors: Ahmed, M. / Goldgur, Y. / Hu, J. / Guo, H.F. / Cheung, N.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vfg.cif.gz | 108 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vfg.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 3vfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vf/3vfg ftp://data.pdbj.org/pub/pdb/validation_reports/vf/3vfg | HTTPS FTP |
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-Related structure data
Related structure data | 2ajuS 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: 23250.695 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: 23400.424 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) |
#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: 2.28 Å3/Da / Density % sol: 46.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Hamptom Index D7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 50590 / Num. obs: 49781 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2AJU Resolution: 1.65→28.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.134 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.259 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→28.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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