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- PDB-6st4: Crystal structure of the tick chemokine-binding protein Evasin-4 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6st4 | ||||||
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Title | Crystal structure of the tick chemokine-binding protein Evasin-4 (SG 1) | ||||||
![]() | Evasin-4 | ||||||
![]() | IMMUNE SYSTEM / CHEMOKINE-BINDING PROTEIN / TICKS | ||||||
Function / homology | negative regulation of chemokine activity / Evasins Class A / Evasins Class A / C-C chemokine binding / Immunoglobulin-like domain / extracellular region / Evasin-4![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ramirez-Escudero, M. / Janssen, B.J.C. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural characterization of anti-CCL5 activity of the tick salivary protein evasin-4. Authors: Denisov, S.S. / Ramirez-Escudero, M. / Heinzmann, A.C.A. / Ippel, J.H. / Dawson, P.E. / Koenen, R.R. / Hackeng, T.M. / Janssen, B.J.C. / Dijkgraaf, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50 KB | Display | ![]() |
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PDB format | ![]() | 37.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.6 KB | Display | ![]() |
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Full document | ![]() | 444.4 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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
#1: Protein | Mass: 11316.322 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 40% ethylene glycol, 0.2 M (NH4)2SO4, 0.1 M Phosphate-citrate pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→58.89 Å / Num. obs: 28221 / % possible obs: 99.99 % / Redundancy: 9.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.143 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.29→1.32 Å / Rmerge(I) obs: 0.1511 / Num. unique obs: 2050 / CC1/2: 0.552 |
-Phasing
Phasing |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 134.32 Å2 / Biso mean: 29.285 Å2 / Biso min: 13.43 Å2
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Refinement step | Cycle: final / Resolution: 1.29→58.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.29→1.323 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.6151 Å / Origin y: 49.3452 Å / Origin z: 1.1446 Å
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