+Open data
-Basic information
Entry | Database: PDB / ID: 7jjf | ||||||
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Title | Sarcin-ricin loop with modified residue. | ||||||
Components | RNA/DNA (27-mer) | ||||||
Keywords | DNA-RNA HYBRID / sarcin-ricin loop / RNA crystal structure / RNA tetraloops / RNA | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Harp, J.M. / Pallan, P.S. / Egli, M. | ||||||
Citation | Journal: Biochemistry / Year: 2020 Title: Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost. Authors: Pallan, P.S. / Lybrand, T.P. / Schlegel, M.K. / Harp, J.M. / Jahns, H. / Manoharan, M. / Egli, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jjf.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jjf.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jjf_validation.pdf.gz | 399.5 KB | Display | wwPDB validaton report |
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Full document | 7jjf_full_validation.pdf.gz | 399.6 KB | Display | |
Data in XML | 7jjf_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 7jjf_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/7jjf ftp://data.pdbj.org/pub/pdb/validation_reports/jj/7jjf | HTTPS FTP |
-Related structure data
Related structure data | 7jjdC 7jjeC 3dvzS S: Starting model for refinement C: citing same article (ref.) |
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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: RNA chain | Mass: 8726.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: RNA was dissolved in 1 mM Na2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0) to attain 350 uM final RNA concentration. The RNA sample was annealed by heating at 65 C for 2 min and slowly cooling ...Details: RNA was dissolved in 1 mM Na2 EDTA (pH 8.0) and 10 mM Tris-HCl (pH 8.0) to attain 350 uM final RNA concentration. The RNA sample was annealed by heating at 65 C for 2 min and slowly cooling to room temperature. Crystallization set-ups were made by mixing 4 uL of RNA solution with 2 uL of a crystallization buffer composed of 3.0 M ammonium sulfate, 10 mM magnesium chloride, 10 mM manganese chloride, and 50 mM potassium 3-(N-morpholino) propanesulfonic acid (MOPS), pH 7.0 at 18 C. Crystals appear in about two weeks time. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.3418 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Mar 19, 2020 |
Radiation | Monochromator: multi-layer confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3418 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→27.36 Å / % possible obs: 94.1 % / Redundancy: 17 % / Biso Wilson estimate: 4.79 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.47 |
Reflection shell | Resolution: 1.2→1.24 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DVZ Resolution: 1.2→27.36 Å / Cross valid method: FREE R-VALUE / σ(F): 4.58 / Phase error: 41.508 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: 10.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→27.36 Å
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Refine LS restraints |
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LS refinement shell |
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