+Open data
-Basic information
Entry | Database: PDB / ID: 1ar2 | ||||||
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Title | DISULFIDE-FREE IMMUNOGLOBULIN FRAGMENT | ||||||
Components | REI | ||||||
Keywords | IMMUNOGLOBULIN / DISULFIDE-FREE / IMMUNOGLOBULIN FRAGMENT / BENCE-JONES | ||||||
Function / homology | Function and homology information 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 / antigen binding ...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 / antigen binding / 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 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Uson, I. / Bes, M.T. / Sheldrick, G.M. / Schneider, T.R. / Hartsch, T. / Fritz, H.-J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ar2.cif.gz | 28.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ar2.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ar2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/1ar2 ftp://data.pdbj.org/pub/pdb/validation_reports/ar/1ar2 | HTTPS FTP |
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-Related structure data
Related structure data | 1reiS S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01607, UniProt: P01593*PLUS |
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#2: 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: 2.67 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.901 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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