+Open data
-Basic information
Entry | Database: PDB / ID: 1emt | ||||||
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Title | FAB ANTIBODY FRAGMENT OF AN C60 ANTIFULLERENE ANTIBODY | ||||||
Components |
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Keywords | IMMUNE SYSTEM / anti-fullerene antibody / nanotubes | ||||||
Function / homology | Function and homology information humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.25 Å | ||||||
Authors | Braden, B.C. / Goldbaum, F.A. / Chen, B.-X. / Erlanger, B.F. / Kirschner, A.N. / Wilson, S.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: X-ray crystal structure of an anti-Buckminsterfullerene antibody fab fragment: biomolecular recognition of C(60). Authors: Braden, B.C. / Goldbaum, F.A. / Chen, B.X. / Kirschner, A.N. / Wilson, S.R. / Erlanger, B.F. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: Antigenicity of Fullerenes: Antibodies Specific for Fullerenes and Their Characteristics Authors: Chen, B.-X. / Wilson, S.R. / Das, M. / Couglin, D.J. / Erlanger, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1emt.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1emt.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 1emt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1emt ftp://data.pdbj.org/pub/pdb/validation_reports/em/1emt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a heterodimer composed of the light (L) and heavy (H) chains |
-Components
#1: Antibody | Mass: 23785.111 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS |
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#2: Antibody | Mass: 22671.557 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5 Details: 10% PEG 8000, 0.1 M citrate, Fab at 7 mg/ml concentration, pH 5.0, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.25 Å / Num. all: 21736 / Num. obs: 19413 / % possible obs: 90 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09 |
Reflection | *PLUS % possible obs: 90 % |
-Processing
Software |
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Refinement | Resolution: 2.25→60 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.25→60 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 60 Å / σ(F): 1 / Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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