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Yorodumi- PDB-6tfh: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tfh | ||||||
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Title | Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH); soaking with Manganese(II) (Mn2+) | ||||||
Components | Chains: A | ||||||
Keywords | RNA / RNA structure / Riboswitch / X-ray crystallography / Non-coding RNA | ||||||
Function / homology | : / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Candidatus Koribacter versatilis Ellin345 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 6tfh.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tfh.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/6tfh ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tfh | HTTPS FTP |
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-Related structure data
Related structure data | 6tb7C 6tf0SC 6tf1C 6tf2C 6tf3C 6tfeC 6tffC 6tfgC S: Starting model for refinement 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
#1: RNA chain | Mass: 16863.957 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Candidatus Koribacter versatilis Ellin345 (bacteria) | ||||||
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#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-NAD / | #4: Chemical | ChemComp-NA / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: 6.8 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: I03 / Wavelength: 1.8923 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8923 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→48.5 Å / Num. obs: 12163 / % possible obs: 96.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 93.67 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.059 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.95→3 Å / Rmerge(I) obs: 2.7 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 359 / CC1/2: 0.48 / Rpim(I) all: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TF0 Resolution: 2.95→48.49 Å / SU ML: 0.5932 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.5261
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 113.5 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→48.49 Å
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Refine LS restraints |
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LS refinement shell |
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