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Yorodumi- PDB-6gaj: Crystal structure of the T1L reovirus sigma1 coiled coil tail (iodide) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gaj | ||||||
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Title | Crystal structure of the T1L reovirus sigma1 coiled coil tail (iodide) | ||||||
Components | Outer capsid protein sigma-1 | ||||||
Keywords | VIRAL PROTEIN / cell attachment protein / reovirus sigma1 / coiled coil | ||||||
Function / homology | Function and homology information viral outer capsid / viral capsid / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | Mammalian orthoreovirus 1 Lang | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å | ||||||
Authors | Dietrich, M.H. / Stehle, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Virol. / Year: 2018 Title: Structural and Functional Features of the Reovirus sigma 1 Tail. Authors: Dietrich, M.H. / Ogden, K.M. / Long, J.M. / Ebenhoch, R. / Thor, A. / Dermody, T.S. / Stehle, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gaj.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gaj.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 6gaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/6gaj ftp://data.pdbj.org/pub/pdb/validation_reports/ga/6gaj | HTTPS FTP |
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-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: 14296.860 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mammalian orthoreovirus 1 Lang / Gene: S1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04506 #2: Chemical | #3: Chemical | ChemComp-CL / #4: 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: 2.04 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 18% (v/v) PEG8000, 0.1M CAPS pH 9.5, 0.2M NaI |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→48.73 Å / Num. obs: 76273 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 12.04 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5563 / CC1/2: 0.723 / Rrim(I) all: 0.876 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→48.73 Å / Cor.coef. Fo:Fc: 0.9488 / Cor.coef. Fo:Fc free: 0.9443 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.062
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Displacement parameters | Biso mean: 15.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.148 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.35→48.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.39 Å / Total num. of bins used: 20
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