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- PDB-6tfe: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tfe | ||||||
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Title | Crystal structure of the ADP-binding domain of the NAD+ riboswitch with N6-Methyl-adenosine-5'-triphosphate (m6ATP) | ||||||
![]() | Chains: A | ||||||
![]() | RNA / RNA structure / Riboswitch / X-ray crystallography / Non-coding RNA | ||||||
Function / homology | BROMIDE ION / N6-Methyladenosine 5'-triphosphate / : / RNA / RNA (> 10)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, L. / Lilley, D.M.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and ligand binding of the ADP-binding domain of the NAD+ riboswitch. Authors: Huang, L. / Wang, J. / Lilley, D.M.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.7 KB | Display | ![]() |
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PDB format | ![]() | 66.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 690.3 KB | Display | ![]() |
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Full document | ![]() | 692.4 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tb7C ![]() 6tf0C ![]() 6tf1C ![]() 6tf2C ![]() 6tf3C ![]() 6tffC ![]() 6tfgC ![]() 6tfhC 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 , 1 types, 1 molecules A
#1: RNA chain | Mass: 16785.062 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() References: GenBank: 94549081 |
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-Non-polymers , 5 types, 42 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/N6E.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/N6E.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-N6E / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 7.2, 10% w/v Polyethylene Glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.52 Å / Num. obs: 27515 / % possible obs: 99.17 % / Redundancy: 6.3 % / Biso Wilson estimate: 71.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.023 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 1.82 / Mean I/σ(I) obs: 1 / Num. unique obs: 697 / CC1/2: 0.59 / Rpim(I) all: 0.76 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→47.52 Å
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Refine LS restraints |
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LS refinement shell |
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