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Yorodumi- PDB-6tf2: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tf2 | ||||||
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Title | Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine 5-triphosphate (ATP) | ||||||
Components | Chains: A | ||||||
Keywords | RNA / RNA structure / Riboswitch / X-ray crystallography | ||||||
Function / homology | ADENOSINE-5'-TRIPHOSPHATE / BROMIDE ION / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Candidatus Koribacter versatilis Ellin345 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||
Authors | Huang, L. / Lilley, D.M.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Rna / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tf2.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tf2.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 6tf2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tf2_validation.pdf.gz | 705.5 KB | Display | wwPDB validaton report |
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Full document | 6tf2_full_validation.pdf.gz | 706.6 KB | Display | |
Data in XML | 6tf2_validation.xml.gz | 4.6 KB | Display | |
Data in CIF | 6tf2_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/6tf2 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tf2 | HTTPS FTP |
-Related structure data
Related structure data | 6tb7C 6tf0C 6tf1C 6tf3C 6tfeC 6tffC 6tfgC 6tfhC 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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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.) Candidatus Koribacter versatilis Ellin345 (bacteria) References: GenBank: 94549081 |
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-Non-polymers , 5 types, 13 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 5.02 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 6.8, 10% w/v Polyethylene Glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9186 Å |
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: 2.49→54.98 Å / Num. obs: 20079 / % possible obs: 98.7 % / Redundancy: 6.27 % / Biso Wilson estimate: 77.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Net I/σ(I): 18.21 |
Reflection shell | Resolution: 2.49→2.53 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 563 / CC1/2: 0.35 / Rpim(I) all: 1 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→54.98 Å / SU ML: 0.4709 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2513
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→54.98 Å
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Refine LS restraints |
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LS refinement shell |
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