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Yorodumi- PDB-7eaf: Crystal structure of SAM-I riboswitch with the Actinomyces-1 k-turn -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eaf | |||||||||
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Title | Crystal structure of SAM-I riboswitch with the Actinomyces-1 k-turn | |||||||||
Components | RNA (94-MER) | |||||||||
Keywords | RNA / SAM / Riboswitch | |||||||||
Function / homology | : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Huang, L. / Lilley, D.M.J. | |||||||||
Funding support | China, United Kingdom, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules. Authors: Huang, L. / Liao, X. / Li, M. / Wang, J. / Peng, X. / Wilson, T.J. / Lilley, D.M.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eaf.cif.gz | 137.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eaf.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 7eaf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/7eaf ftp://data.pdbj.org/pub/pdb/validation_reports/ea/7eaf | HTTPS FTP |
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-Related structure data
Related structure data | 7eagC 5fk3S 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 30519.307 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||
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#2: Chemical | ChemComp-SAM / | ||||||
#3: Chemical | ChemComp-BA / #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40 MM NA-CACODYLATE (PH 7.0), 80 MM KCL, 40 MM BACL2, 12 MM SPERMINE-HCL, 12% (V/V) MPD. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 7963 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 66.96 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.056 / Rrim(I) all: 0.154 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1123 / CC1/2: 0.771 / Rpim(I) all: 0.656 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FK3 Resolution: 2.85→29.22 Å / SU ML: 0.4498 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.4143 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: 75.22 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→29.22 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.32676536 Å / Origin y: -9.95773684407 Å / Origin z: -23.0866878138 Å
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Refinement TLS group | Selection details: all |