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Yorodumi- PDB-1fdl: CRYSTALLOGRAPHIC REFINEMENT OF THE THREE-DIMENSIONAL STRUCTURE OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fdl | ||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT OF THE THREE-DIMENSIONAL STRUCTURE OF THE FAB D1.3-LYSOZYME COMPLEX AT 2.5-ANGSTROMS RESOLUTION | ||||||
Components |
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Keywords | COMPLEX (ANTIBODY-ANTIGEN) | ||||||
Function / homology | Function and homology information 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 / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...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 / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 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 / external side of plasma membrane / 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 / Resolution: 2.5 Å | ||||||
Authors | Fischmann, T.O. / Poljak, R.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1991 Title: Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution. Authors: Fischmann, T.O. / Bentley, G.A. / Bhat, T.N. / Boulot, G. / Mariuzza, R.A. / Phillips, S.E. / Tello, D. / Poljak, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fdl.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fdl.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 1fdl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fdl ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fdl | 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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Atom site foot note | 1: RESIDUES PRO L 8, PRO L 95, PRO L 141, PRO H 150, PRO H 152 AND PRO H 192 ARE CIS PROLINES. |
-Components
#1: Antibody | Mass: 23677.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: GenBank: 2072141, UniProt: P01837*PLUS |
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#2: Antibody | Mass: 23398.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Organ: EGG / Production host: Escherichia coli (E. coli) / References: UniProt: P01868*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) / References: UniProt: P00698, lysozyme |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.77 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 170.1055-1058 / PH range low: 7 / PH range high: 6 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 5.5 Å / Num. obs: 20475 / Num. measured all: 41026 / Rmerge(I) obs: 2.5 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Rfactor Rwork: 0.184 / Highest resolution: 2.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor all: 0.195 / Rfactor obs: 0.184 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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