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Open data
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Basic information
Entry | Database: PDB / ID: 1ar2 | ||||||
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Title | DISULFIDE-FREE IMMUNOGLOBULIN FRAGMENT | ||||||
![]() | REI | ||||||
![]() | IMMUNOGLOBULIN / DISULFIDE-FREE / IMMUNOGLOBULIN FRAGMENT / BENCE-JONES | ||||||
Function / homology | ![]() CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Uson, I. / Bes, M.T. / Sheldrick, G.M. / Schneider, T.R. / Hartsch, T. / Fritz, H.-J. | ||||||
![]() | ![]() Title: X-ray crystallography reveals stringent conservation of protein fold after removal of the only disulfide bridge from a stabilized immunoglobulin variable domain. Authors: Uson, I. / Bes, M.T. / Sheldrick, G.M. / Schneider, T.R. / Hartsch, T. / Fritz, H.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.9 KB | Display | ![]() |
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PDB format | ![]() | 21.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 411.6 KB | Display | ![]() |
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Full document | ![]() | 415.9 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1reiS S: Starting model for refinement |
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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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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 11921.168 Da / Num. of mol.: 1 / Fragment: VARIABLE REGION, LIGHT CHAIN / Mutation: INS(TP-1D), C25V, Y34H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 4.6 Details: VAPOUR DIFFUSION AL 4 C FROM A PROTEIN SOLUTION CONTAINING 8 MG/ML IN 50 MM POTASSIUM PHOSPHATE BUFFER AL PH 7, USING 2 M AMMONIUM SULFATE IN 100 MM SODIUM ACETATE BUFFER, PH 4.6, vapor ...Details: VAPOUR DIFFUSION AL 4 C FROM A PROTEIN SOLUTION CONTAINING 8 MG/ML IN 50 MM POTASSIUM PHOSPHATE BUFFER AL PH 7, USING 2 M AMMONIUM SULFATE IN 100 MM SODIUM ACETATE BUFFER, PH 4.6, vapor diffusion, temperature 277K PH range: 4.6-7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1996 / Details: BENT CRYSTAL MONOCHROMATOR |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→75 Å / Num. obs: 3549 / % possible obs: 97 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.104 / Rsym value: 0.088 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.43 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 37985 |
Reflection shell | *PLUS % possible obs: 97.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1REI Resolution: 2.8→75 Å / Num. parameters: 3434 / Num. restraintsaints: 4775 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: SIMULATED ANNEALING WITH X-PLOR, FINAL REFINEMENT WITH SHELXL-97
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 819 / Occupancy sum non hydrogen: 857.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→75 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 75 Å / Rfactor all: 0.28 / Rfactor obs: 0.228 / Rfactor Rfree: 0.343 / Rfactor Rwork: 0.2543 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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