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- PDB-8utg: An RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome -
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Open data
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Basic information
Entry | Database: PDB / ID: 8utg | |||||||||||||||||||||||||||||||||||||
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Title | An RNA G-Quadruplex from the NS5 gene in the West Nile Virus Genome | |||||||||||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / RNA Quadruplex / G-Quadruplex / G-tetrad / West Nile Virus / Orthoflavivirus | Function / homology | : / AMMONIUM ION / RNA / RNA (> 10) | ![]() Biological species | ![]() Method | ![]() ![]() ![]() ![]() Terrell, J.R. / Le, T.T. / Wilson, W.D. / Siemer, J.L. | Funding support | | ![]()
![]() ![]() Title: Structure of an RNA G-quadruplex from the West Nile virus genome. Authors: Terrell, J.R. / Le, T.T. / Paul, A. / Brinton, M.A. / Wilson, W.D. / Poon, G.M.K. / Germann, M.W. / Siemer, J.L. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.9 KB | Display | ![]() |
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PDB format | ![]() | 53.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: U / Beg label comp-ID: U / End auth comp-ID: U / End label comp-ID: U / Auth seq-ID: 1 / Label seq-ID: 1
NCS oper: (Code: givenMatrix: (0.971509729087, -0.0247860338485, 0.2357000187), (-0.0253816548387, -0.999677705292, -0.000507088737204), (0.23563662255, -0.00548981487841, -0.971825727199)Vector: 2. ...NCS oper: (Code: given Matrix: (0.971509729087, -0.0247860338485, 0.2357000187), Vector: |
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Components
#1: RNA chain | Mass: 6850.101 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Sitting-drop tray prepared 1:1 using an Art Robbins Crystal Gryphon. Molecular Dimensions Helix HT condition F4 (50mM KCl, 50mM Bis-Tris pH=7.0, 1.1M ammonium sulfate) yielded loopable ...Details: Sitting-drop tray prepared 1:1 using an Art Robbins Crystal Gryphon. Molecular Dimensions Helix HT condition F4 (50mM KCl, 50mM Bis-Tris pH=7.0, 1.1M ammonium sulfate) yielded loopable crystals after 6 weeks. Crystals were directly flash frozen without cryoprotection |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 25, 2023 |
Radiation | Monochromator: Horizontal double crystal monochromator (DCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→29.28 Å / Num. obs: 8368 / % possible obs: 99.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 41.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.039 / Rrim(I) all: 0.148 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.97→2.02 Å / Redundancy: 14.8 % / Rmerge(I) obs: 3.286 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 567 / CC1/2: 0.831 / Rpim(I) all: 0.85 / Rrim(I) all: 3.397 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→29.28 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.12272322381 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -14.0899780457 Å / Origin y: -2.73395615904 Å / Origin z: -13.195263151 Å
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Refinement TLS group | Selection details: all |