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Yorodumi- PDB-6st4: Crystal structure of the tick chemokine-binding protein Evasin-4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6st4 | ||||||
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Title | Crystal structure of the tick chemokine-binding protein Evasin-4 (SG 1) | ||||||
Components | Evasin-4 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Rhipicephalus sanguineus (brown dog tick) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.29 Å | ||||||
Authors | Ramirez-Escudero, M. / Janssen, B.J.C. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6st4.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6st4.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 6st4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6st4_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 6st4_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 6st4_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 6st4_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6st4 ftp://data.pdbj.org/pub/pdb/validation_reports/st/6st4 | HTTPS FTP |
-Related structure data
-Links
-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.) Rhipicephalus sanguineus (brown dog tick) Production host: Escherichia coli (E. coli) / References: UniProt: P0C8E9 | ||||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9772 Å |
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: SAD / Resolution: 1.29→58.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.838 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.043 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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