+Open data
-Basic information
Entry | Database: PDB / ID: 3eyu | ||||||
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Title | PFA1 Fab fragment complexed with Ror2(518-525) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / amyloid / alzheimer's / protein-peptide complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.71 Å | ||||||
Authors | Gardberg, A.S. / Dealwis, C.G. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structures of Abeta-related peptide--monoclonal antibody complexes. Authors: Gardberg, A. / Dice, L. / Pridgen, K. / Ko, J. / Patterson, P. / Ou, S. / Wetzel, R. / Dealwis, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eyu.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyu.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 3eyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyu ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyu | HTTPS FTP |
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-Related 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: 24203.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Hybridoma culture / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igk-C / Production host: Mus musculus (house mouse) / Strain (production host): BALB C / References: UniProt: A2NHM3 |
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#2: Antibody | Mass: 24210.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Hybridoma culture / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / Strain (production host): BALB C |
#3: Protein/peptide | Mass: 1076.143 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The peptide is chemically synthesized. It is identical to fragment from Homo sapiens receptor-related neurotrophic tyrosine kinase (ROR2). |
#4: 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: 2.09 Å3/Da / Density % sol: 41.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 20% w/v PEG3350, 0.2 M LiCl, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→21.29 Å / Num. obs: 9216 / % possible obs: 84.79 % |
Reflection shell | Resolution: 2.709→2.778 Å / % possible all: 45.48 |
-Processing
Software |
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Refinement | Resolution: 2.71→21.29 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 1 / SU B: 32.157 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.451 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 46.41 Å2 / Biso mean: 32.305 Å2 / Biso min: 12.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→21.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.709→2.778 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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