+Open data
-Basic information
Entry | Database: PDB / ID: 8te0 | |||||||||
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Title | 16mer self-complementary duplex RNA with D:C pair sequence 1 | |||||||||
Components | RNA | |||||||||
Keywords | RNA / Diaminopurine / Non-canonical base pair | |||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | |||||||||
Authors | Fang, Z. / Jia, X. / Szostak, J.W. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2024 Title: Diaminopurine in Nonenzymatic RNA Template Copying. Authors: Jia, X. / Fang, Z. / Kim, S.C. / Ding, D. / Zhou, L. / Szostak, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8te0.cif.gz | 24.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8te0.ent.gz | 13.7 KB | Display | PDB format |
PDBx/mmJSON format | 8te0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8te0_validation.pdf.gz | 399.5 KB | Display | wwPDB validaton report |
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Full document | 8te0_full_validation.pdf.gz | 400.2 KB | Display | |
Data in XML | 8te0_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 8te0_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/8te0 ftp://data.pdbj.org/pub/pdb/validation_reports/te/8te0 | HTTPS FTP |
-Related structure data
Related structure data | 8tdyC 8tdzC 8te2C 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: 5097.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Chemical | ChemComp-MG / |
#3: 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: 2.22 Å3/Da / Density % sol: 44.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10 mM Magnesium chloride hexahydrate, 50 mM HEPES sodium pH 7.0, 4.0 M Lithium chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.033216 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033216 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→50 Å / Num. obs: 8586 / % possible obs: 96.2 % / Redundancy: 7.1 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.024 / Rrim(I) all: 0.069 / Χ2: 0.919 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 2 % / Rmerge(I) obs: 0.268 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 267 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.214 / Rrim(I) all: 0.345 / Χ2: 0.804 / % possible all: 64.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→35.414 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.485 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.082 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.558 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→35.414 Å
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Refine LS restraints |
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LS refinement shell |
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