+Open data
-Basic information
Entry | Database: PDB / ID: 6idh | ||||||
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Title | Antibody 64M-5 Fab in ligand-free form | ||||||
Components |
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Keywords | IMMUNE SYSTEM / DNA (6-4) PHOTOPRODUCT / IMMUNOGLOBULIN / FAB | ||||||
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 | 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 | 6idh.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6idh.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 6idh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6idh_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 6idh_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | 6idh_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 6idh_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6idh ftp://data.pdbj.org/pub/pdb/validation_reports/id/6idh | HTTPS FTP |
-Related structure data
Related structure data | 6idgC 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: 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: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18% PEG3350, 0.1 M sodium acetate, 0.1 M sodium cacodylate (pH 6.5) |
-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: Jan 27, 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: 2.5→30 Å / Num. obs: 17067 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1641 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EHL Resolution: 2.5→28.63 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 87697.66 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Bsol: 36.9683 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2.5→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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