+Open data
-Basic information
Entry | Database: PDB / ID: 6i31 | ||||||
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Title | Crystal structure of the tick chemokine-binding protein Evasin-3 | ||||||
Components | Evasin-3 | ||||||
Keywords | PEPTIDE BINDING PROTEIN / chemokine-binding tick evasin saliva | ||||||
Function / homology | negative regulation of protein homodimerization activity / negative regulation of chemokine activity / C-X-C chemokine binding / extracellular region / : / Evasin-3 Function and homology information | ||||||
Biological species | Rhipicephalus sanguineus (brown dog tick) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.79 Å | ||||||
Authors | Dias, J.M. / Shaw, J.P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: A knottin scaffold directs the CXC-chemokine-binding specificity of tick evasins. Authors: Lee, A.W. / Deruaz, M. / Lynch, C. / Davies, G. / Singh, K. / Alenazi, Y. / Eaton, J.R.O. / Kawamura, A. / Shaw, J. / Proudfoot, A.E.I. / Dias, J.M. / Bhattacharya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i31.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i31.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 6i31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i31 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i31 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 7012.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhipicephalus sanguineus (brown dog tick) Production host: Escherichia coli (E. coli) / References: UniProt: P0C8E8 #2: Chemical | ChemComp-CD / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 25%PEG3350 100mM Bis-tris buffer pH 6.5 20mM CdCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.977 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 31, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→47.62 Å / Num. obs: 11993 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 26.31 Å2 / Rsym value: 0.066 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.79→1.97 Å |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.79→14.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.1
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Displacement parameters | Biso mean: 42.33 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.79→14.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.97 Å / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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