+Open data
-Basic information
Entry | Database: PDB / ID: 5e2u | ||||||
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Title | Structure of anti-TAU AT8 FAB in the presence of phosphopeptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Malia, T. / Teplyakov, A. | ||||||
Citation | Journal: Proteins / Year: 2016 Title: Epitope mapping and structural basis for the recognition of phosphorylated tau by the anti-tau antibody AT8. Authors: Malia, T.J. / Teplyakov, A. / Ernst, R. / Wu, S.J. / Lacy, E.R. / Liu, X. / Vandermeeren, M. / Mercken, M. / Luo, J. / Sweet, R.W. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e2u.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e2u.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e2u_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 5e2u_full_validation.pdf.gz | 448.7 KB | Display | |
Data in XML | 5e2u_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 5e2u_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e2/5e2u ftp://data.pdbj.org/pub/pdb/validation_reports/e2/5e2u | HTTPS FTP |
-Related structure data
Related structure data | 5e2tC 5e2vC 5e2wC 1ml8S 3leyS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 24031.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24099.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
#3: Chemical | ChemComp-SO4 / |
#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: 2.87 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20% PEG 3350, 0.2 M AMMONIUM SULFATE, 15% PEG 4000, 0.2 M AMMONIUM SULFATE, 24% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 3, 2012 / Details: VARIMAX HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 21800 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.7 / % possible all: 95.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1ML8 and 3LEY Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.312 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.242
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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