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Open data
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Basic information
Entry | Database: PDB / ID: 6kdi | ||||||
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Title | Antibody 64M-5 Fab including isoAsp in complex with dT(6-4)T | ||||||
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![]() | IMMUNE SYSTEM / DNA (6-4) PHOTOPRODUCT / IMMUNOGLOBULIN / FAB / isoaspartate | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biochemical basis of the formation of isoaspartate in the complementarity-determining region of antibody 64M-5 Fab. Authors: Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N. #1: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.8 KB | Display | ![]() |
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PDB format | ![]() | 74.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 449.9 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kdhC ![]() 1ehlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 24097.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23828.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: DNA chain | Mass: 565.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 15% PEG2000, 0.1 M ammonium sulfate, 0.1 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 105 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 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: 2.7→30 Å / Num. obs: 12638 / % possible obs: 95.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 967 / % possible all: 75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EHL Resolution: 2.7→27.29 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 57157 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Bsol: 32.7839 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.4 Å2 / Biso mean: 37.9 Å2 / Biso min: 7.04 Å2
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Refine analyze |
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Refinement step | Cycle: final / Resolution: 2.7→27.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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