+Open data
-Basic information
Entry | Database: PDB / ID: 1rfd | ||||||
---|---|---|---|---|---|---|---|
Title | ANTI-COCAINE ANTIBODY M82G2 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / ANTI-COCAINE ANTIBODY / FAB | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Pozharski, E. / Hewagama, A. / Shanafelt, A.B. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Diversity in hapten recognition: structural study of an anti-cocaine antibody M82G2. Authors: Pozharski, E. / Moulin, A. / Hewagama, A. / Shanafelt, A.B. / Petsko, G.A. / Ringe, D. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE NO DATABASE REFERENCE SEQUENCE WAS FOUND FOR EITHER PROTEIN IN THIS STRUCTURE AT THE TIME ...SEQUENCE NO DATABASE REFERENCE SEQUENCE WAS FOUND FOR EITHER PROTEIN IN THIS STRUCTURE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rfd.cif.gz | 101.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rfd.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 1rfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rfd_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rfd_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 1rfd_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 1rfd_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/1rfd ftp://data.pdbj.org/pub/pdb/validation_reports/rf/1rfd | HTTPS FTP |
-Related structure data
Related structure data | 1q72C 1qygSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 23884.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
---|---|
#2: Antibody | Mass: 23519.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.39 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 2M AMMONIUM SULFATE, 5% ISO-PROPANOL, pH 5.20, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→30 Å / Num. all: 26932 / Num. obs: 26932 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2603 / % possible all: 88.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QYG Resolution: 2.09→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MASK CORRECTED TO EXCLUDE INTERNAL CAVITIES
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 0.303 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→30 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.09→2.16 Å
|