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Yorodumi- PDB-3pp3: Epitope characterization and crystal structure of GA101 provide i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pp3 | ||||||
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Title | Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for the type I / type II distinction of anti- CD20 antibodies | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody Fab-fragment Ig-domain / antibody / CD20 | ||||||
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: 2.508 Å | ||||||
Authors | Hopfner, K.-P. / Lammens, A. | ||||||
Citation | Journal: Blood / Year: 2011 Title: Epitope characterization and crystal structure of GA101 provide insights into the molecular basis for type I/II distinction of CD20 antibodies. Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / ...Authors: Niederfellner, G. / Lammens, A. / Mundigl, O. / Georges, G.J. / Schaefer, W. / Schwaiger, M. / Franke, A. / Wiechmann, K. / Jenewein, S. / Slootstra, J.W. / Timmerman, P. / Brannstrom, A. / Lindstrom, F. / Mossner, E. / Umana, P. / Hopfner, K.P. / Klein, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pp3.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pp3.ent.gz | 148.5 KB | Display | PDB format |
PDBx/mmJSON format | 3pp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/3pp3 ftp://data.pdbj.org/pub/pdb/validation_reports/pp/3pp3 | HTTPS FTP |
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-Related structure data
Related structure data | 3pp4C 1t04S 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23969.881 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster) #2: Antibody | Mass: 23964.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Chinese hamster ovary (CHO) / Production host: Cricetulus griseus (Chinese hamster) #3: 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: 2.41 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 24% (w/v) PEG4000, 0.15 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2008 |
Radiation | Monochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 32252 / Num. obs: 31465 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.105 / Rsym value: 0.067 / Net I/σ(I): 12.42 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.277 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T04 Resolution: 2.508→25 Å / SU ML: 0.4 / σ(F): 1.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.581 Å2 / ksol: 0.341 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.508→25 Å
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Refine LS restraints |
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LS refinement shell |
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