+Open data
-Basic information
Entry | Database: PDB / ID: 1ehl | ||||||
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Title | 64M-2 ANTIBODY FAB COMPLEXED WITH D(5HT)(6-4)T | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN / PROTEIN-DNA COMPLEX / DNA PHOTOPRODUCT | ||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Yokoyama, H. / Mizutani, R. / Satow, Y. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation. Authors: Yokoyama, H. / Mizutani, R. / Satow, Y. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O. #1: Journal: Photochem.Photobiol. / Year: 1991 Title: Simultaneous Establishment of Monoclonal Antibodies Specific for Either Cyclobutane Pyrimidine Dimer or (6-4)photoproduct from the Same Mouse Immunized with Ultraviolet-Irradiated DNA Authors: Mori, T. / Nakane, M. / Hattori, T. / Matsunaga, T. / Ihara, M. / Nikaido, O. #2: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1998 Title: Antibodies Specific for (6-4) DNA Photoproducts: Cloning, Antibody Modeling and Construction of a Single-Chain Fv Derivative Authors: Morioka, H. / Miura, H. / Kobayashi, H. / Koizumi, T. / Fujii, K. / Asano, K. / Matsunaga, T. / Nikaido, O. / Stewart, J.D. / Ohtsuka, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ehl.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ehl.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ehl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ehl_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 1ehl_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 1ehl_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 1ehl_validation.cif.gz | 35.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1ehl ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1ehl | HTTPS FTP |
-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
#1: DNA chain | Mass: 501.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Purified from ultraviolet-radiated dTpT |
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#2: Antibody | Mass: 23891.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: UniProt: P01837*PLUS |
#3: Antibody | Mass: 23522.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: UniProt: P01863*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, nickel chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / PH range low: 8.4 / PH range high: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 26, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.7 Å / Num. all: 77929 / Num. obs: 18790 / % possible obs: 93.5 % / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.221 / Num. unique all: 1571 / % possible all: 79.1 |
Reflection | *PLUS Num. measured all: 77929 |
Reflection shell | *PLUS % possible obs: 79.1 % / Num. unique obs: 1571 / Num. measured obs: 4271 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 10 Å / σ(F): 1 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.49 Å / Rfactor Rfree: 0.359 / Rfactor obs: 0.296 |