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Yorodumi- PDB-1dqj: CRYSTAL STRUCTURE OF THE ANTI-LYSOZYME ANTIBODY HYHEL-63 COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dqj | ||||||
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Title | CRYSTAL STRUCTURE OF THE ANTI-LYSOZYME ANTIBODY HYHEL-63 COMPLEXED WITH HEN EGG WHITE LYSOZYME | ||||||
Components |
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Keywords | immune system/hydrolase / antibody / protein-protein complex / hen egg white lysozyme / immune system-hydrolase COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment ...positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / multivesicular body / B cell differentiation / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / response to bacterium / positive regulation of immune response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / antibacterial humoral response / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Li, H. / Mariuzza, R.A. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,). Authors: Li, Y. / Li, H. / Smith-Gill, S.J. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqj.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqj.ent.gz | 102 KB | Display | PDB format |
PDBx/mmJSON format | 1dqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqj ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqj | HTTPS FTP |
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-Related 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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Details | The biological assembly is a heterodimer with heavy and light chains |
-Components
#1: Antibody | Mass: 23583.869 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: GenBank: 2950241, UniProt: P01837*PLUS |
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#2: Antibody | Mass: 22556.023 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01865*PLUS |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM / Plasmid: PPIC9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698, lysozyme |
#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: 2.54 Å3/Da / Density % sol: 51.65 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4K, Ammonium acetate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 5, 1998 |
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→100 Å / Num. obs: 45762 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.371 / % possible all: 85 |
Reflection | *PLUS Num. obs: 45762 / Num. measured all: 366760 |
Reflection shell | *PLUS % possible obs: 85 % / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Resolution: 2→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→100 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.249 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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