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Yorodumi- PDB-1ndg: Crystal structure of Fab fragment of antibody HyHEL-8 complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ndg | ||||||
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Title | Crystal structure of Fab fragment of antibody HyHEL-8 complexed with its antigen lysozyme | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HYDROLASE / antibody / lysozyme / mutant / HyHEL-8 / IMMUNE SYSTEM-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport / phagocytosis, engulfment ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport / phagocytosis, engulfment / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / multivesicular body / B cell differentiation / complement activation, classical pathway / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / antigen binding / beta-N-acetylglucosaminidase activity / response to bacterium / positive regulation of immune response / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / antibacterial humoral response / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mariuzza, R.A. / Li, Y. / Li, H. / Yang, F. / Smith-Gill, S.J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: X-ray snapshots of the maturation of an antibody response to a protein antigen Authors: Li, Y. / Li, H. / Yang, F. / 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 | 1ndg.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ndg.ent.gz | 102.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ndg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ndg_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 1ndg_full_validation.pdf.gz | 457.9 KB | Display | |
Data in XML | 1ndg_validation.xml.gz | 28 KB | Display | |
Data in CIF | 1ndg_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1ndg ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1ndg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23583.869 Da / Num. of mol.: 1 / Fragment: light chain Source method: isolated from a genetically manipulated source Details: first chain of Anti-Lysozyme Antibody HyHEL-8 / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01837 |
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#2: Antibody | Mass: 22726.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: second chain of Anti-Lysozyme Antibody HyHEL-8 / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01865 |
#3: Protein | Mass: 14245.045 Da / Num. of mol.: 1 / Mutation: R61A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PPIC9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698, lysozyme |
#4: Chemical | ChemComp-ACY / |
#5: 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: 2.25 Å3/Da / Density % sol: 44.8 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B |
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Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→33.32 Å / Num. all: 46457 / Num. obs: 46457 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.2 Å2 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 46465 / % possible obs: 95 % / Num. measured all: 403172 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 80.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.32 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4249343.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1758 Å2 / ksol: 0.365696 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze | Luzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→33.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.254 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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