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- PDB-8hna: Crystal structure of N-terminal fragment (20-221aa) of human SCARF1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hna | ||||||
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Title | Crystal structure of N-terminal fragment (20-221aa) of human SCARF1 | ||||||
![]() | Scavenger receptor class F member 1 | ||||||
![]() | LIPID BINDING PROTEIN / ![]() | ||||||
Function / homology | ![]() low-density lipoprotein particle binding / scavenger receptor activity / Scavenging by Class F Receptors / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron remodeling / positive regulation of axon regeneration / dendrite development / cholesterol catabolic process / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y. / He, Y. / Li, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of N-terminal of SCARF1 at 2.6 Angstroms resolution Authors: Wang, Y. / He, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.8 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 23042.059 Da / Num. of mol.: 1 / Fragment: N-terminal 20-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.72 Å3/Da / Density % sol: 73.94 % |
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Crystal grow![]() | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M citric acid/sodium citrate (pH 3.6), 9% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→30 Å / Num. obs: 14015 / % possible obs: 99.1 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 32.125 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.78 / Num. unique obs: 1299 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→26.89 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 22.9095 Å / Origin y: 82.6801 Å / Origin z: 36.7246 Å
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Refinement TLS group | Selection details: all |