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- PDB-7d7x: Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d7x | ||||||
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Title | Crystal Structure of the Domain1 of NAD+ Riboswitch with adenosine diphosphate (ADP) | ||||||
![]() | 18GAAA(52-MER) | ||||||
![]() | RNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography | ||||||
Function / homology | ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, H. / Ren, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding. Authors: Chen, H. / Egger, M. / Xu, X. / Flemmich, L. / Krasheninina, O. / Sun, A. / Micura, R. / Ren, 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 | ![]() | 45 KB | Display | ![]() |
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PDB format | ![]() | 29.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d7vSC ![]() 7d7wC ![]() 7d7yC ![]() 7d7zC ![]() 7d81C ![]() 7d82C S: Starting model for refinement 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
#1: RNA chain | Mass: 16438.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||
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#2: Chemical | ChemComp-GTP / | ||||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.75 Å3/Da / Density % sol: 74.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 1.6 M MgSO4 |
-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: Jan 13, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.631→50 Å / Num. obs: 9705 / % possible obs: 99.9 % / Redundancy: 12 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Χ2: 0.773 / Net I/σ(I): 4.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D7V Resolution: 2.631→26.636 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.53 / Stereochemistry target values: ML
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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 max: 152.72 Å2 / Biso mean: 79.8285 Å2 / Biso min: 57.31 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.631→26.636 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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