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Open data
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Basic information
Entry | Database: PDB / ID: 3uaf | ||||||
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Title | Crystal Structure of a TTR-52 mutant of C. elegans | ||||||
![]() | TTR-52 | ||||||
![]() | PROTEIN BINDING / beta barrel/sandwich / cell engulfment / secreted | ||||||
Function / homology | ![]() recognition of apoptotic cell / aminophospholipid transport / scavenger receptor binding / apoptotic process involved in development / phosphatidylserine binding / extracellular vesicle / protein-macromolecule adaptor activity / cell surface / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kang, Y.Y. / Zhao, D.F. / Liang, H.H. / Liu, B. / Liu, Q.W. / Wang, X.C. / Liu, Y.F. | ||||||
![]() | ![]() Title: Structural study of TTR-52 reveals the mechanism by which a bridging molecule mediates apoptotic cell engulfment Authors: Kang, Y.Y. / Zhao, D.F. / Liang, H.H. / Liu, B. / Zhang, Y. / Liu, Q.W. / Wang, X.C. / Liu, Y.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.7 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.1 KB | Display | ![]() |
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Full document | ![]() | 424.7 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: Protein | Mass: 13042.625 Da / Num. of mol.: 1 / Fragment: residues 21-135 / Mutation: E50A,D51A,S52A,L53A,P54A,L55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.23 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 4.5 Details: 0.2M ammonium sulfate, 0.1M soldium acetate, 35% PEGME2000, pH 4.5, EVAPORATION, temperature 289K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.01→50 Å / Num. obs: 7360 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 19.23 Å2 | |||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.481 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.79 Å2 / Biso mean: 21.2378 Å2 / Biso min: 8.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.01→33.655 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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