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Yorodumi- PDB-3vw3: Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vw3 | ||||||
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Title | Antibody 64M-5 Fab in complex with a double-stranded DNA (6-4) photoproduct | ||||||
Components |
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Keywords | IMMUNE SYSTEM/DNA / Protein-DNA complex / DNA (6-4) photoproduct / Immunoglobulin / IMMUNE SYSTEM-DNA complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / COBALT HEXAMMINE(III) / DNA / DNA (> 10) Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yokoyama, H. / Mizutani, R. / Satow, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / 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. #1: 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. #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 | 3vw3.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vw3.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vw3_validation.pdf.gz | 468.5 KB | Display | wwPDB validaton report |
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Full document | 3vw3_full_validation.pdf.gz | 484.2 KB | Display | |
Data in XML | 3vw3_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 3vw3_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/3vw3 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/3vw3 | HTTPS FTP |
-Related structure data
Related structure data | 1kegS 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
-DNA chain , 2 types, 2 molecules AB
#3: DNA chain | Mass: 5638.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA with (6-4) photoproduct |
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#4: DNA chain | Mass: 5396.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic DNA |
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23993.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c |
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#2: Antibody | Mass: 23713.553 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c |
-Non-polymers , 2 types, 145 molecules
#5: Chemical | ChemComp-NCO / |
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#6: 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: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 12% PEG 3350, 0.1M magnesium acetate, 10mM Cobalt hexamine chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.8 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 1, 2002 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 20541 / % possible obs: 97.1 % / Redundancy: 10.5 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 60.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 16 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KEG Resolution: 2.5→28.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 573129.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.1259 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→28.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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