+Open data
-Basic information
Entry | Database: PDB / ID: 6idg | ||||||
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Title | antibody 64M-5 Fab in complex with dT(6-4)T | ||||||
Components |
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Keywords | IMMUNE SYSTEM / DNA (6-4) PHOTOPRODUCT / IMMUNOGLOBULIN / FAB | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA Function and homology information | ||||||
Biological species | Mus musculus (house mouse) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2019 Title: Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms. Authors: Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013 Title: Structure of a double-stranded DNA (6-4) photoproduct in complex with the 64M-5 antibody Fab Authors: Yokoyama, H. / Mizutani, R. / Satow, Y. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6idg.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6idg.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 6idg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6idg ftp://data.pdbj.org/pub/pdb/validation_reports/id/6idg | HTTPS FTP |
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-Related structure data
Related structure data | 6idhC 1ehlS S: Starting model for refinement C: citing same article (ref.) |
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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: Antibody | Mass: 23993.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma / Strain: BALB/c |
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#2: Antibody | Mass: 23828.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: hybridoma / Strain: BALB/c |
#3: DNA chain | Mass: 565.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: 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: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10% PEG2000, 0.5 M lithium sulfate, 0.1 M sodium citrate (pH 3.5) |
-Data collection
Diffraction | Mean temperature: 105 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: Apr 22, 2000 |
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→30 Å / Num. obs: 27037 / % possible obs: 88.2 % / Redundancy: 11.4 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 31.8 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 2018 / % possible all: 66.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EHL Resolution: 2→28.18 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 72552.57 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Bsol: 56.1635 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2→28.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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