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Yorodumi- PDB-5jie: Crystal structure of the Orsay virus delta protein N-terminal fra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jie | ||||||
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Title | Crystal structure of the Orsay virus delta protein N-terminal fragment (aa 1~66) | ||||||
Components | Protein delta | ||||||
Keywords | VIRAL PROTEIN / Delta protein / Orsay virus / C. elegans / helical | ||||||
Function / homology | Protein delta Function and homology information | ||||||
Biological species | Orsay virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1374 Å | ||||||
Authors | Fan, Y. / Guo, Y. / Zhong, W. / Tao, Y.J. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2017 Title: Structure of a pentameric virion-associated fiber with a potential role in Orsay virus entry to host cells. Authors: Fan, Y. / Guo, Y.R. / Yuan, W. / Zhou, Y. / Holt, M.V. / Wang, T. / Demeler, B. / Young, N.L. / Zhong, W. / Tao, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jie.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jie.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jie_validation.pdf.gz | 447.8 KB | Display | wwPDB validaton report |
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Full document | 5jie_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 5jie_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 5jie_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/5jie ftp://data.pdbj.org/pub/pdb/validation_reports/ji/5jie | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 7338.308 Da / Num. of mol.: 5 / Fragment: UNP residues 1-66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orsay virus / Production host: Escherichia coli (E. coli) / References: UniProt: E9KNV6 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.137→50 Å / Num. obs: 19535 / % possible obs: 95.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.122 / Net I/av σ(I): 11.738 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1374→48.018 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.72 Å2 / Biso mean: 35.3721 Å2 / Biso min: 18.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1374→48.018 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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