+Open data
-Basic information
Entry | Database: PDB / ID: 6kdi | ||||||
---|---|---|---|---|---|---|---|
Title | Antibody 64M-5 Fab including isoAsp in complex with dT(6-4)T | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / DNA (6-4) PHOTOPRODUCT / IMMUNOGLOBULIN / FAB / isoaspartate | ||||||
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: 2.7 Å | ||||||
Authors | Yokoyama, H. / Mizutani, R. / Noguchi, S. / Hayashida, N. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Sci Rep / Year: 2019 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: Journal: Acta Crystallogr F Struct Biol Commun / 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6kdi.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kdi.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kdi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kdi_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6kdi_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 6kdi_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6kdi_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/6kdi ftp://data.pdbj.org/pub/pdb/validation_reports/kd/6kdi | HTTPS FTP |
-Related structure data
Related structure data | 6kdhC 1ehlS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24097.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: Hybridoma / Strain: BALB/c |
---|---|
#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 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→27.29 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|