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Yorodumi- PDB-2ddq: Crystal Structure of the Fab fragment of a R310 antibody complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ddq | ||||||
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Title | Crystal Structure of the Fab fragment of a R310 antibody complexed with (R)-HNE-histidine adduct | ||||||
Components |
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Keywords | IMMUNE SYSTEM / monoclonal antibody / 4-hydroxy-2-nonenal / immunoglobulin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Ito, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Bispecific abs against modified protein and DNA with oxidized lipids Authors: Akagawa, M. / Ito, S. / Toyoda, K. / Ishii, Y. / Tatsuda, E. / Shibata, T. / Yamaguchi, S. / Kawai, Y. / Ishino, K. / Kishi, Y. / Adachi, T. / Tsubata, T. / Takasaki, Y. / Hattori, N. / Matsuda, T. / Uchida, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and molecular-replacement studies of the monoclonal antibody mAbR310 specific for the (R)-HNE-modified protein Authors: Ito, S. / Tatsuda, E. / Ishino, K. / Suzuki, K. / Sakai, H. / Uchida, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ddq.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ddq.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ddq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/2ddq ftp://data.pdbj.org/pub/pdb/validation_reports/dd/2ddq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 22771.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JL75 |
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#2: Antibody | Mass: 24043.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-EPE / |
#4: Chemical | ChemComp-HRB / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.2 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→35.9 Å / Num. obs: 18734 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 35.4 Å2 |
Reflection shell | Highest resolution: 2.35 Å / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→35.83 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1391391.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.3405 Å2 / ksol: 0.43856 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→35.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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