+Open data
-Basic information
Entry | Database: PDB / ID: 1yed | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4) | ||||||
Components | (IGG1 FAB FRAGMENT (D.2.4)) x 2 | ||||||
Keywords | CATALYTIC ANTIBODY / TRANSITION STATE ANALOGUE | ||||||
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 / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Golinelli-Pimpaneau, B. / Knossow, M. | ||||||
Citation | Journal: Science / Year: 1997 Title: Structural convergence in the active sites of a family of catalytic antibodies. Authors: Charbonnier, J.B. / Golinelli-Pimpaneau, B. / Gigant, B. / Tawfik, D.S. / Chap, R. / Schindler, D.G. / Kim, S.H. / Green, B.S. / Eshhar, Z. / Knossow, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yed.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yed.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yed.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1yed ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1yed | HTTPS FTP |
---|
-Related structure data
Related structure data | 1yecSC 1yeeC 1dfbS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.054319, -0.998513, -0.004603), Vector: |
-Components
#1: Antibody | Mass: 24092.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TRANSITION STATE ANALOGUE / Source: (natural) Mus musculus (house mouse) / References: PIR: S16112 #2: Antibody | Mass: 24499.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TRANSITION STATE ANALOGUE / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.88 % |
---|---|
Crystal grow | pH: 7 / Details: pH 7.0 |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.375 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 12, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.375 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 18722 / % possible obs: 87.6 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.071 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YEC FOR THE VARIABLE DOMAINS AND PDB ENTRY 1DFB FOR THE CONSTANT DOMAINS Resolution: 3.1→7 Å / σ(F): 2 Details: RESIDUES POORLY DEFINED BY THE ELECTRON DENSITY: CHAINS L, A: 1, 157 - 160, 198 - 207, 220 - 222 CHAINS H, B: 129 - 137, 173 - 175, 187 - 193, 214 - 217
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|