+Open data
-Basic information
Entry | Database: PDB / ID: 8sxl | ||||||||||||||||||||||||||||
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Title | RNA UU template binding to AMP monomer | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / AMP | Function / homology | ADENOSINE MONOPHOSPHATE / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | Authors | Zhang, W. / Dantsu, Y. | Funding support | 1items |
Citation | Journal: Rsc Chem Biol / Year: 2023 | Title: Insight into the structures of unusual base pairs in RNA complexes containing a primer/template/adenosine ligand. Authors: Dantsu, Y. / Zhang, Y. / Zhang, W. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sxl.cif.gz | 30.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sxl.ent.gz | 19.6 KB | Display | PDB format |
PDBx/mmJSON format | 8sxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/8sxl ftp://data.pdbj.org/pub/pdb/validation_reports/sx/8sxl | HTTPS FTP |
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-Related structure data
Related structure data | 8swgSC 8swoC 8sx5C 8sx6C 8sy1C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4485.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.36 Å3/Da / Density % sol: 47.8 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% v/v MPD, 0.040 M sodium cacodylate trihydrate, pH 7.0, 0.012 M spermine tetrahydrochloride, 0.020 M magnesium chloride hexahydrate |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9785 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Mar 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 7680 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.087 / Χ2: 0.525 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 737 / CC1/2: 0.911 / CC star: 0.976 / Χ2: 0.848 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8SWG Resolution: 1.9→37.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.556 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.881 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→37.99 Å
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Refine LS restraints |
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