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Open data
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Basic information
Entry | Database: PDB / ID: 1emt | ||||||
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Title | FAB ANTIBODY FRAGMENT OF AN C60 ANTIFULLERENE ANTIBODY | ||||||
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![]() | IMMUNE SYSTEM / anti-fullerene antibody / nanotubes | ||||||
Function / homology | ![]() 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 / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / 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 / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Braden, B.C. / Goldbaum, F.A. / Chen, B.-X. / Erlanger, B.F. / Kirschner, A.N. / Wilson, S.R. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373.1 KB | Display | ![]() |
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Full document | ![]() | 387.8 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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 |
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Components
#1: Antibody | Mass: 23785.111 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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) ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 % |
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Processing
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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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