+Open data
-Basic information
Entry | Database: PDB / ID: 7bxv | ||||||
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Title | 11A1 antibody-peptide complex | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex with peptide | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Irie, K. / Irie, Y. / Kita, A. / Miki, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biorxiv / Year: 2022 Title: APOE epsilon 4 allele advances the age-dependent decline of amyloid beta clearance in the human cortex. Authors: Saito, A. / Kageyama, Y. / Pletnikova, O. / Rudow, G.L. / An, Y. / Irie, Y. / Kita, A. / Miki, K. / Li, L. / Southall, P. / Irie, K. / Troncoso, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bxv.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bxv.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 7bxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bxv_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7bxv_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7bxv_validation.xml.gz | 22 KB | Display | |
Data in CIF | 7bxv_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/7bxv ftp://data.pdbj.org/pub/pdb/validation_reports/bx/7bxv | HTTPS FTP |
-Related structure data
Related structure data | 1mnuS 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
#1: Antibody | Mass: 23873.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||
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#2: Antibody | Mass: 23769.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) | ||||
#3: Protein/peptide | Mass: 685.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3,350, NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. obs: 44761 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.068 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.135 / Num. unique obs: 2456 / Rpim(I) all: 0.056 / Rrim(I) all: 0.147 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MNU Resolution: 1.75→45.074 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.989 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.104
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.057 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→45.074 Å
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Refine LS restraints |
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LS refinement shell |
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