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Yorodumi- PDB-1c12: INSIGHT IN ODORANT PERCEPTION: THE CRYSTAL STRUCTURE AND BINDING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c12 | ||||||
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Title | INSIGHT IN ODORANT PERCEPTION: THE CRYSTAL STRUCTURE AND BINDING CHARACTERISTICS OF ANTIBODY FRAGMENTS DIRECTED AGAINST THE MUSK ODORANT TRASEOLIDE | ||||||
Components | (PROTEIN (ANTIBODY FRAGMENT FAB)) x 2 | ||||||
Keywords | IMMUNE SYSTEM / ANTIBODY-ANTIGEN COMPLEX / SCFV FRAGMENT / CDRH3 / MUSK ODORANT / ODORANT SPECIFICITY | ||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / 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 / IgG immunoglobulin complex / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / 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: 2.6 Å | ||||||
Authors | Langedijk, A.C. / Spinelli, S. / Anguille, C. / Hermans, P. / Nederlof, J. / Butenandt, J. / Honegger, A. / Cambillau, C. / Pluckthun, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Insight into odorant perception: the crystal structure and binding characteristics of antibody fragments directed against the musk odorant traseolide. Authors: Langedijk, A.C. / Spinelli, S. / Anguille, C. / Hermans, P. / Nederlof, J. / Butenandt, J. / Honegger, A. / Cambillau, C. / Pluckthun, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c12.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c12.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/1c12 ftp://data.pdbj.org/pub/pdb/validation_reports/c1/1c12 | 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 Fab monomer |
-Components
#1: Antibody | Mass: 23391.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01837*PLUS |
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#2: Antibody | Mass: 23841.791 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01869*PLUS |
#3: Chemical | ChemComp-TRZ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.05 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: PEG 8000, SODIUM ACETATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 20.0K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 47 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 5, 1995 |
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→20 Å / Num. obs: 15749 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.3 / % possible all: 55 |
Reflection shell | *PLUS % possible obs: 55 % |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.6→12 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.6→12 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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