+Open data
-Basic information
Entry | Database: PDB / ID: 8sx6 | ||||||||||||||||||||||||||||
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Title | RNA duplex bound with GMP and AMP monomers | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / GMP / AMP | Function / homology | ADENOSINE MONOPHOSPHATE / GUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 | 8sx6.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sx6.ent.gz | 21.1 KB | Display | PDB format |
PDBx/mmJSON format | 8sx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sx6_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8sx6_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8sx6_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 8sx6_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/8sx6 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/8sx6 | HTTPS FTP |
-Related structure data
Related structure data | 8swgC 8swoC 8sx5C 8sxlC 8sy1C 6c8nS 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: 4513.789 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-AMP / | #5: 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: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% v/v MPD, 0.040 M sodium cacodylate trihydrate, pH 7.0, 0.012 M Spermine tetrahydrochloride, 0.08 M sodium chloride, 0.012 M potassium chloride, 0.02 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: 0.987 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: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 15931 / % possible obs: 98.5 % / Redundancy: 10.7 % / CC1/2: 0.978 / CC star: 0.994 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.042 / Rrim(I) all: 0.129 / Χ2: 0.965 / Net I/σ(I): 121.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 1584 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.169 / Rrim(I) all: 0.558 / Χ2: 0.978 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6C8N Resolution: 1.45→26.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.235 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / 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: 27.869 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→26.73 Å
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Refine LS restraints |
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