+Open data
-Basic information
Entry | Database: PDB / ID: 1keg | ||||||
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Title | Antibody 64M-2 Fab complexed with dTT(6-4)TT | ||||||
Components |
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Keywords | IMMUNE SYSTEM/DNA / protein-DNA complex / DNA photoproduct / immunoglobulin / IMMUNE SYSTEM-DNA COMPLEX | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NICKEL (II) ION / DNA Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Yokoyama, H. / Mizutani, R. / Satow, Y. / Sato, K. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structure of the DNA (6-4) photoproduct dTT(6-4)TT in complex with the 64M-2 antibody Fab fragment implies increased antibody-binding affinity by the flanking nucleotides. Authors: Yokoyama, H. / Mizutani, R. / Satow, Y. / Sato, K. / Komatsu, Y. / Ohtsuka, E. / Nikaido, O. #1: 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. #2: 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 Ultraviolet-irradiated DNA Authors: Mori, T. / Nakane, M. / Hattori, T. / Matsunaga, T. / Ihara, M. / Nikaido, O. | ||||||
History |
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Remark 600 | HETEROGEN There is a C6-C4 bond between 64T residue 2 and T residue 3 of chain A. The 64T linked to ...HETEROGEN There is a C6-C4 bond between 64T residue 2 and T residue 3 of chain A. The 64T linked to T is referred to as DT(6-4)T. | ||||||
Remark 999 | SEQUENCE THE NUCLEOTIDE SEQUENCES WHICH ENCODE FOR CHAINS L AND H ARE LISTED IN GB ENTRIES E08525 ...SEQUENCE THE NUCLEOTIDE SEQUENCES WHICH ENCODE FOR CHAINS L AND H ARE LISTED IN GB ENTRIES E08525 (22-330) AND E08524 (7-330) RESPECTIVELY. The residue numbering of chains L and H is non-sequential. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1keg.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1keg.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 1keg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/1keg ftp://data.pdbj.org/pub/pdb/validation_reports/ke/1keg | HTTPS FTP |
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-Related structure data
Related structure data | 1ehlS 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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-Components
#1: DNA chain | Mass: 1189.830 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The chain was synthesized by coupling thymidines to both sides of dT(6-4)T which was purified from ultraviolet-radiated dTpT. |
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#2: Antibody | Mass: 23762.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: Balb/c |
#3: Antibody | Mass: 23679.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma / Strain: Balb/c |
#4: Chemical | ChemComp-NI / |
#5: 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: 2.57 Å3/Da / Density % sol: 52.22 % | ||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, nickel chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1998 |
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: 2.4→29.6 Å / Num. all: 18057 / Num. obs: 17570 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3 / Num. unique all: 1607 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EHL Resolution: 2.4→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 22 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å
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