[English] 日本語
Yorodumi- PDB-2a6d: Crystal structure analysis of the anti-arsonate germline antibody... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Germline / FAB / ANTIBODY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M. | ||||||
Citation | Journal: Immunity / Year: 2006 Title: Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Authors: Sethi, D.K. / Agarwal, A. / Manivel, V. / Rao, K.V. / Salunke, D.M. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS ...SEQUENCE THE SEQUENCE IS NOT DEPOSITED IN ANY SEQUENCE DATABASE EXCEPT RESIDUES 1 TO 120 OF CHAINS B,H WHICH CORRESPOND TO DEPOSITED SEQUENCE OF THE HEAVY CHAIN VARIABLE REGION OF ANTI-ARSONATE ANTIBODY 36-65 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2a6d.cif.gz | 176.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2a6d.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a6d_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2a6d_full_validation.pdf.gz | 510.7 KB | Display | |
Data in XML | 2a6d_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2a6d_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6d ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6d | HTTPS FTP |
-Related structure data
Related structure data | 2a6iC 2a6jC 2a6kC 6fabS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23707.049 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse) / Strain: A/J #2: Antibody | Mass: 23942.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Mouse monoclonal / Source: (natural) Mus musculus (house mouse) #3: Protein/peptide | | Mass: 1365.578 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: chemically synthesized (Phage display derived peptide) #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.8 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 18% PEG 8000, cacodylate, 0.05% azide, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→100 Å / Num. all: 23421 / Num. obs: 23421 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.87 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FAB Resolution: 2.9→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→100 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|