+Open data
-Basic information
Entry | Database: PDB / ID: 1y0l | ||||||
---|---|---|---|---|---|---|---|
Title | Catalytic elimination antibody 34E4 in complex with hapten | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / CATALYTIC ANTIBODY / CHIMERIC FAB / HAPTEN COMPLEX | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HAN Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Debler, E.W. / Ito, S. / Heine, A. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structural origins of efficient proton abstraction from carbon by a catalytic antibody Authors: Debler, E.W. / Ito, S. / Seebeck, F.P. / Heine, A. / Hilvert, D. / Wilson, I.A. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE SEQUENCES OF THE FAB COMPLEXES ARE NOT YET AVAILABLE IN ANY REFERENCE SEQUENCE DATABASES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1y0l.cif.gz | 350.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1y0l.ent.gz | 285.2 KB | Display | PDB format |
PDBx/mmJSON format | 1y0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y0l_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1y0l_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1y0l_validation.xml.gz | 67.9 KB | Display | |
Data in CIF | 1y0l_validation.cif.gz | 93.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y0/1y0l ftp://data.pdbj.org/pub/pdb/validation_reports/y0/1y0l | HTTPS FTP |
-Related structure data
Related structure data | 1y18C 1mrcS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 BIOLOGICAL MOLECULES: LH, AB, CD, and EF. |
-Components
#1: Antibody | Mass: 23258.826 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THE VARIABLE DOMAIN (RESIDUES 1-107) IS FROM A MURINE SOURCE AND THE CONSTANT DOMAIN (RESIDUES 108-214) IS FROM A HUMAN SOURCE. Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 #2: Antibody | Mass: 24586.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: THE VARIABLE DOMAIN (RESIDUES 1-113) IS FROM A MURINE SOURCE AND THE CONSTANT DOMAIN (RESIDUES 114-233) IS FROM A HUMAN SOURCE. Source: (gene. exp.) Mus musculus, Homo sapiens / Genus: Mus, Homo / Species: , / Strain: , / Plasmid: p4xH-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 #3: Chemical | ChemComp-HAN / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.9 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.5M Diammonium hydrogen phosphate, 0.5M NaCl, 0.1M imidazole HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2003 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 83376 / Num. obs: 81375 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 29.8 Å2 / Rsym value: 0.066 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.75 / Num. unique all: 4054 / % possible all: 98.4 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MRC Resolution: 2.5→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.54 Å / Rfactor Rfree error: 0.013
|