+Open data
-Basic information
Entry | Database: PDB / ID: 1lo0 | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic Retro-Diels-Alderase Transition State Analogue Complex | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / catalytic antibody / Fab fragment | ||||||
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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / antigen processing and presentation / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / multivesicular body / antigen binding / B cell differentiation / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hugot, M. / Reymond, J.L. / Baumann, U. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: A structural basis for the activity of retro-Diels-Alder catalytic antibodies: evidence for a catalytic aromatic residue. Authors: Hugot, M. / Bensel, N. / Vogel, M. / Reymond, M.T. / Stadler, B. / Reymond, J.L. / Baumann, U. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE At the time of processing, this sequence has not yet been deposited in a sequence database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lo0.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lo0.ent.gz | 134.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lo0 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lo0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1lo2C 1lo3C 1lo4C 28b4S 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 domain: (Details: RESTRAINED) |
-Components
#1: Antibody | Mass: 24268.992 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source Details: The antibodies were isolated from hybridoma cells and Fab fragments were generated by papain digestion. Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837, UniProt: A2NHM3*PLUS #2: Antibody | Mass: 23704.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: The antibodies were isolated from hybridoma cells and Fab fragments were generated by papain digestion. Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: Yale mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→30.3 Å / Num. obs: 78457 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.77→1.85 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 9.9 / Rsym value: 0.136 / % possible all: 0.959 |
Reflection | *PLUS Num. obs: 74192 / % possible obs: 81.7 % / Num. measured all: 1025225 |
Reflection shell | *PLUS % possible obs: 95.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 28B4 Resolution: 2→30.3 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: CRYSTALS ARE PSEUDO-MEROHEDRALLY TWINNED TWINNING LAW H,-K,-L TWINNING FRACTION 0.3787
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: SOLVENT MASK / Bsol: 36.9 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.3 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.256 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|