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Yorodumi- PDB-6tf0: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tf0 | ||||||
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Title | Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Nicotinamide adenine dinucleotide, reduced (NADH) | ||||||
Components | Chains: A | ||||||
Keywords | RNA / RNA structure / tRNA-mimicking / X-ray crystallography | ||||||
Function / homology | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Candidatus Koribacter versatilis Ellin345 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 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 | 6tf0.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tf0.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 6tf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tf0_validation.pdf.gz | 689 KB | Display | wwPDB validaton report |
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Full document | 6tf0_full_validation.pdf.gz | 691.2 KB | Display | |
Data in XML | 6tf0_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 6tf0_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/6tf0 ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tf0 | HTTPS FTP |
-Related structure data
Related structure data | 6tb7C 6tf1C 6tf2C 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
#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-MG / #3: Chemical | #4: Chemical | ChemComp-NAI / | #5: Water | ChemComp-HOH / | 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: 5.02 Å3/Da / Density % sol: 75.5 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 6.6, 10% w/v Polyethylene Glycol 3350 (30% PEG200) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9195 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: 0.9195 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→32.11 Å / Num. obs: 36174 / % possible obs: 98.81 % / Observed criterion σ(I): 1.2 / Redundancy: 6.6 % / Biso Wilson estimate: 65.88 Å2 / CC1/2: 0.8 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.016 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.1→2.14 Å / Rmerge(I) obs: 1.44 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 939 / CC1/2: 0.8 / Rpim(I) all: 0.59 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→32.11 Å / SU ML: 0.3171 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.5277
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→32.11 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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