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Yorodumi- PDB-2aab: Structural basis of antigen mimicry in a clinically relevant mela... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aab | ||||||
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Title | Structural basis of antigen mimicry in a clinically relevant melanoma antigen system | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Anti-idiotypic antibody / molecular mimicry / melanoma / immunotherapy | ||||||
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: 2.5 Å | ||||||
Authors | Chang, C.-C. / Hernandez-Guzman, F.G. / Luo, W. / Wang, X. / Ferrone, S. / Ghosh, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structural basis of antigen mimicry in a clinically relevant melanoma antigen system. Authors: Chang, C.-C. / Hernandez-Guzman, F.G. / Luo, W. / Wang, X. / Ferrone, S. / Ghosh, D. | ||||||
History |
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Remark 999 | SEQUENCE an appropriate sequence database reference was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aab.cif.gz | 98 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aab.ent.gz | 73.6 KB | Display | PDB format |
PDBx/mmJSON format | 2aab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2aab_validation.pdf.gz | 373.9 KB | Display | wwPDB validaton report |
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Full document | 2aab_full_validation.pdf.gz | 388.3 KB | Display | |
Data in XML | 2aab_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 2aab_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/2aab ftp://data.pdbj.org/pub/pdb/validation_reports/aa/2aab | HTTPS FTP |
-Related structure data
Related structure data | 2rscS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monoclonal antibody fragment Fab' consisting of a light chain L and a heavy chain H |
-Components
#1: Antibody | Mass: 23993.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
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#2: Antibody | Mass: 26233.570 Da / Num. of mol.: 1 / Fragment: Fab fragment / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2002 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33 Å / Num. all: 17003 / Num. obs: 16656 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 4.2 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RSC Resolution: 2.5→33 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.34 Å / Luzzati sigma a obs: 0.31 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→33 Å
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Refine LS restraints |
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