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Yorodumi- PDB-6stc: Crystal structure of the tick chemokine-binding protein Evasin-4 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6stc | ||||||
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Title | Crystal structure of the tick chemokine-binding protein Evasin-4 (SG 2) | ||||||
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 / ACETATE ION / DI(HYDROXYETHYL)ETHER / Evasin-4 Function and homology information | ||||||
Biological species | Rhipicephalus sanguineus (brown dog tick) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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 | 6stc.cif.gz | 51.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6stc.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 6stc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6stc_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 6stc_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 6stc_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | 6stc_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6stc ftp://data.pdbj.org/pub/pdb/validation_reports/st/6stc | HTTPS FTP |
-Related structure data
Related structure data | 6st4SC 6steC 6stkC S: Starting model for refinement C: citing same article (ref.) |
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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
#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 | #3: Chemical | #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: 2.77 Å3/Da / Density % sol: 55.66 % / Description: hexagonal prism |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 40% PEG 400, 0.1 M NaAc pH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→43.06 Å / Num. obs: 14083 / % possible obs: 98.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.69→1.72 Å / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 722 / CC1/2: 0.496 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ST4 Resolution: 1.69→30.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.99 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.082 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 83.19 Å2 / Biso mean: 32.411 Å2 / Biso min: 22.03 Å2
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Refinement step | Cycle: final / Resolution: 1.69→30.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -26.639 Å / Origin y: 25.688 Å / Origin z: 9.112 Å
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