[English] 日本語
Yorodumi- PDB-4fab: THREE-DIMENSIONAL STRUCTURE OF A FLUORESCEIN-FAB COMPLEX CRYSTALL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fab | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | THREE-DIMENSIONAL STRUCTURE OF A FLUORESCEIN-FAB COMPLEX CRYSTALLIZED IN 2-METHYL-2,4-PENTANEDIOL | |||||||||
Components |
| |||||||||
Keywords | IMMUNOGLOBULIN | |||||||||
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 / Fc-gamma receptor I complex binding / 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 / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / endosome to lysosome transport / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | |||||||||
Authors | Herron, J.N. / He, X. / Mason, M.L. / Vossjunior, E.W. / Edmundson, A.B. | |||||||||
Citation | Journal: Proteins / Year: 1989 Title: Three-dimensional structure of a fluorescein-Fab complex crystallized in 2-methyl-2,4-pentanediol. Authors: Herron, J.N. / He, X.M. / Mason, M.L. / Voss Jr., E.W. / Edmundson, A.B. #1: Journal: Proteins / Year: 1988 Title: Differences in Crystal Properties and Ligand Affinities of an Antifluorescyl Fab (4-4-20) in Two Solvent Systems Authors: Gibson, A.L. / Herron, J.N. / He, X.-M. / Patrick, V.A. / Mason, M.L. / Lin, J.-N. / Kranz, D.M. / Vossjunior, E.W. / Edmundson, A.B. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4fab.cif.gz | 94 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4fab.ent.gz | 73.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/4fab ftp://data.pdbj.org/pub/pdb/validation_reports/fa/4fab | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO L 8, PRO L 100, PRO L 146, AND PRO H 152 ARE CIS PROLINES. |
-Components
#1: Antibody | Mass: 24187.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1589925 |
---|---|
#2: Antibody | Mass: 23662.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01865 |
#3: Chemical | ChemComp-FLU / |
#4: Chemical | ChemComp-MPD / ( |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 12-14 ℃ / Method: batch method | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 2.7 Å / Num. obs: 11116 |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.7→6 Å / σ(I): 1.5 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |