+Open data
-Basic information
Entry | Database: PDB / ID: 6dmc | ||||||||||||
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Title | ppGpp Riboswitch bound to ppGpp, native structure | ||||||||||||
Components | ppGpp Riboswitch | ||||||||||||
Keywords | RNA / riboswitch / non-coding / yKKC | ||||||||||||
Function / homology | GUANOSINE-5',3'-TETRAPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||||||||
Biological species | Sulfobacillus acidophilus DSM 10332 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||||||||
Authors | Peselis, A. / Serganov, A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands. Authors: Peselis, A. / Serganov, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dmc.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dmc.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dmc_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6dmc_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6dmc_validation.xml.gz | 11 KB | Display | |
Data in CIF | 6dmc_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/6dmc ftp://data.pdbj.org/pub/pdb/validation_reports/dm/6dmc | HTTPS FTP |
-Related structure data
Related structure data | 6dlqC 6dlrC 6dlsC 6dltC 6dmdC 6dmeC 6dnrC 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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2 |
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Unit cell |
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-Components
-RNA chain , 1 types, 2 molecules AB
#1: RNA chain | Mass: 33316.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfobacillus acidophilus DSM 10332 (bacteria) Production host: in vitro transcription vector pT7-TP(deltai) (others) |
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-Non-polymers , 5 types, 202 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.075 M MgCl2, 0.1 M Na-acetate pH 4.2, and 21% PEG400 (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 27688 / % possible obs: 96.1 % / Redundancy: 4 % / CC1/2: 0.54 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.069 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.886 / CC1/2: 0.633 |
-Processing
Software |
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Refinement | Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.76 / SU ML: 0.205 / Cross valid method: FREE R-VALUE / ESU R: 0.304 / ESU R Free: 0.242 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.771 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→20 Å
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Refine LS restraints |
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