[English] 日本語
![](img/lk-miru.gif)
- PDB-1gpo: CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FA... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1gpo | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT | ||||||
![]() | (ANTIBODY M41) x 2 | ||||||
![]() | IMMUNE SYSTEM / PROTEIN ENGINEERING / ANTIBODY DESIGN / IMMUNOGLOBULIN STRUCTURE / ANTIGEN-BINDING SITE / CANONICAL CONFORMATION / COMPLEMENTARITY-DETERMINING REGION | ||||||
Function / homology | ![]() 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 / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / 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 / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schiweck, W. / Skerra, A. | ||||||
![]() | ![]() Title: The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment. Authors: Schiweck, W. / Skerra, A. #1: ![]() Title: Fermenter Production of an Artificial Fab Fragment, Rationally Designed for the Antigen Cystatin, and its Optimized Crystallization Through Constant Domain Shuffling Authors: Schiweck, W. / Skerra, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 191.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 151.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 486.6 KB | Display | |
Data in XML | ![]() | 39.5 KB | Display | |
Data in CIF | ![]() | 57.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.997725, 0.020407, -0.064249), Vector: |
-
Components
#1: Antibody | Mass: 24172.518 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 24182.809 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: 2.0 M AMMONIUM SULFATE, 5 % DMSO, 0.1 M CACODYLATE PH 6.5 | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting dropDetails: Schiweck, W., (1995) Proteins: Struct.,Funct., Genet., 23, 561. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995 |
Radiation | Monochromator: NICKEL FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→60 Å / Num. obs: 69136 / % possible obs: 84.6 % / Observed criterion σ(I): 0.5 / Redundancy: 2.6 % / Rmerge(I) obs: 0.065 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.215 / % possible all: 50.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: HYBRID FAB FRAGMENT CONSISTING OF THE MODELLED STRUCTURE FOR THE ARTIFICIAL FV FRAGMENT M41 AND CONSTANT DOMAINS OF THE ANTI-LYSOZYME ANTIBODY HYHEL-10 Resolution: 1.95→8 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|