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- PDB-6tb7: 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: 6tb7 | ||||||
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Title | Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine monophosphate (AMP) | ||||||
![]() | RNA | ||||||
![]() | RNA / RNA structure / tRNA-mimicking / X-ray crystallography | ||||||
Function / homology | ADENOSINE MONOPHOSPHATE / BROMIDE ION / : / 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 | ![]() | 74.5 KB | Display | ![]() |
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PDB format | ![]() | 53.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tf0C ![]() 6tf1C ![]() 6tf2C ![]() 6tf3C ![]() 6tfeC ![]() 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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1 |
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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, 30 molecules ![](data/chem/img/AMP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AMP / | ||||||
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#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-BR / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.02 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 7.0, 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: 2.53→47.6 Å / Num. obs: 20563 / % possible obs: 98.36 % / Redundancy: 6.2 % / Biso Wilson estimate: 71.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 20.06 |
Reflection shell | Resolution: 2.53→2.57 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 540 / CC1/2: 0.48 / Rpim(I) all: 0.99 / % possible all: 97.7 |
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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: 84.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→47.59 Å
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Refine LS restraints |
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LS refinement shell |
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