+Open data
-Basic information
Entry | Database: PDB / ID: 6cy9 | |||||||||
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Title | SA11 Rotavirus NSP2 with disulfide bridge | |||||||||
Components | Non-structural protein 2 | |||||||||
Keywords | VIRAL PROTEIN / Rotavirus SA11 / NSP2 / Disulfide | |||||||||
Function / homology | Function and homology information nucleoside diphosphate kinase activity / ribonucleoside triphosphate phosphatase activity / viral genome replication / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Rotavirus A | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.615 Å | |||||||||
Authors | Anish, R. / Hu, L. / Sankaran, B. / Prasad, B.V.V. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories. Authors: Criglar, J.M. / Anish, R. / Hu, L. / Crawford, S.E. / Sankaran, B. / Prasad, B.V.V. / Estes, M.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cy9.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cy9.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 6cy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cy9_validation.pdf.gz | 427.3 KB | Display | wwPDB validaton report |
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Full document | 6cy9_full_validation.pdf.gz | 429.3 KB | Display | |
Data in XML | 6cy9_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 6cy9_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cy9 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cy9 | HTTPS FTP |
-Related structure data
Related structure data | 6aukC 6cyaC 1l9vS C: citing same article (ref.) S: Starting model for refinement |
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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: 37084.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rotavirus A / Gene: NSP2 / Production host: Escherichia coli (E. coli) References: UniProt: A2T3N6, UniProt: A2T3P0*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5 mg/mL protein, 0.16 M calcium acetate, 0.08 M sodium cacodylate, 14.4% polyethylene glycol, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999949 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999949 Å / Relative weight: 1 |
Reflection | Resolution: 2.615→45.241 Å / Num. obs: 13423 / % possible obs: 99.06 % / Redundancy: 15.3 % / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.036 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 1.48 / Rpim(I) all: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1L9V Resolution: 2.615→45.241 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.615→45.241 Å
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Refine LS restraints |
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LS refinement shell |
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