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- PDB-6dlq: PRPP Riboswitch bound to PRPP, manganese chloride soaked structure -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dlq | ||||||||||||
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Title | PRPP Riboswitch bound to PRPP, manganese chloride soaked structure | ||||||||||||
![]() | PRPP Riboswitch | ||||||||||||
![]() | RNA / riboswitch / non-coding / yKKC | ||||||||||||
Function / homology | : / : / Chem-PRP / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Peselis, A. / Serganov, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | 52.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.8 KB | Display | ![]() |
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Full document | ![]() | 767.2 KB | Display | |
Data in XML | ![]() | 5.7 KB | Display | |
Data in CIF | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6dlrC ![]() 6dlsC ![]() 6dltC ![]() 6dmcC ![]() 6dmdC ![]() 6dmeC ![]() 6dnrC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-RNA chain / Sugars , 2 types, 2 molecules A![](data/chem/img/PRP.gif)
![](data/chem/img/PRP.gif)
#1: RNA chain | Mass: 34902.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: in vitro transcription vector pT7-TP(deltai) (others) |
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#2: Sugar | ChemComp-PRP / |
-Non-polymers , 4 types, 25 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.11 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M NH4-acetate, 0.1 M HEPES-KOH pH 7.4, and 45% 2-methyl-2,4-pentanediol (v/v) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 21504 / % possible obs: 98.4 % / Redundancy: 5.1 % / CC1/2: 0.987 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.04 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.8→20 Å / Rmerge(I) obs: 0.518 / Rpim(I) all: 0.3269 |
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Processing
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Refinement | Resolution: 2.8→20 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell |
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