+Open data
-Basic information
Entry | Database: PDB / ID: 7kga | ||||||
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Title | Crystal structure of a mosquito-borne flavivirus dumbbell RNA | ||||||
Components | RNA (90-MER) | ||||||
Keywords | RNA / viral RNA / noncoding RNA / flavivirus / viral replication | ||||||
Function / homology | IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Donggang virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Akiyama, B.M. / Graham, M.E. / O'Donoghue, Z. / Beckham, J.D. / Kieft, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Authors: Akiyama, B.M. / Graham, M.E. / O Donoghue, Z. / Beckham, J.D. / Kieft, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kga.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kga.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kga_validation.pdf.gz | 844.1 KB | Display | wwPDB validaton report |
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Full document | 7kga_full_validation.pdf.gz | 847.1 KB | Display | |
Data in XML | 7kga_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7kga_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/7kga ftp://data.pdbj.org/pub/pdb/validation_reports/kg/7kga | HTTPS FTP |
-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: RNA chain | Mass: 28984.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Donggang virus / References: GenBank: 380877198 #2: Chemical | ChemComp-IRI / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.06 Å3/Da / Density % sol: 40.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM Bis-Tris pH 7.0, 25 mM NaCl, 25 mM LiCl, 4.5 mM CaCl2, 50 mM Guanidine HCl, 23.75% polyethylene glycol 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.10208 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Apr 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.10208 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.74 Å / Num. obs: 27633 / % possible obs: 99.81 % / Redundancy: 10.9 % / Biso Wilson estimate: 34.69 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1303 / Rpim(I) all: 0.04105 / Rrim(I) all: 0.1367 / Net I/av σ(I): 17.95 / Net I/σ(I): 17.95 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 10 % / Rmerge(I) obs: 0.8781 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 2741 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.2917 / Rrim(I) all: 0.9265 / % possible all: 99.89 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→44.74 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 148.73 Å2 / Biso mean: 38.6332 Å2 / Biso min: 14.11 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.74 Å
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LS refinement shell | Resolution: 2.1→2.175 Å
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