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- PDB-2agj: Crystal Structure of a glycosylated Fab from an IgM cryoglobulin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2agj | ||||||||||||
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Title | Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody | ||||||||||||
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![]() | IMMUNE SYSTEM / Antibody / Immunoglobulin superfamily / catalytic antibody | ||||||||||||
Function / homology | ![]() hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / immunoglobulin complex, circulating / immunoglobulin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway ...hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / IgM immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / immunoglobulin complex, circulating / immunoglobulin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Cell surface interactions at the vascular wall / antigen binding / B cell receptor signaling pathway / antibacterial humoral response / defense response to Gram-negative bacterium / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / innate immune response / cell surface / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Ramsland, P.A. / Terzyan, S.S. / Cloud, G. / Bourne, C.R. / Farrugia, W. / Tribbick, G. / Geysen, H.M. / Moomaw, C.R. / Slaughter, C.A. / Edmundson, A.B. | ||||||||||||
![]() | ![]() Title: Crystal structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody Authors: Ramsland, P.A. / Terzyan, S.S. / Cloud, G. / Bourne, C.R. / Farrugia, W. / Tribbick, G. / Geysen, H.M. / Moomaw, C.R. / Slaughter, C.A. / Edmundson, A.B. #1: ![]() Title: Interconversion of different crystal forms of Fabs from human IgM cryoglobulins Authors: Ramsland, P.A. / Upshaw, J.L. / Shultz, B.B. / DeWitt, C.R. / Chissoe III, W.F. / Raison, R.L. / Edmundson, A.B. #2: Journal: J.Mol.Recog. / Year: 2002 Title: Dealing with intractable protein cores: protein sequencing of the Mcg IgG and the Yvo IgM heavy chain variable domains Authors: Shaw, D.C. / Shultz, B.B. / Ramsland, P.A. / Edmundson, A.B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 869.6 KB | Display | ![]() |
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Full document | ![]() | 900.4 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
#1: Antibody | Mass: 23367.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Antibody | Mass: 24557.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 15000-20000, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 14, 2002 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→99 Å / Num. all: 18260 / Num. obs: 18260 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.5 % / Biso Wilson estimate: 52.8 Å2 / Rsym value: 0.102 / Net I/σ(I): 32.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Num. unique all: 1742 / Rsym value: 0.854 / % possible all: 95.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IGM 1DN0 Resolution: 2.6→42.2 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→42.2 Å
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Refine LS restraints |
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