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Yorodumi- PDB-8vax: Cadmium catalyzed primer extension product with 14mer primer and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vax | ||||||
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Title | Cadmium catalyzed primer extension product with 14mer primer and mixed phosphorothioate activated G monomer | ||||||
Components | Cadmium catalyzed nonenzymatic RNA primer extension product | ||||||
Keywords | RNA / Phosphorothioate / Cadmium / thiophilic metal ion / nonenzymatic primer extension | ||||||
Function / homology | 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.417 Å | ||||||
Authors | Fang, Z. / Szostak, J.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2024 Title: Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension. Authors: Fang, Z. / Pazienza, L.T. / Zhang, J. / Tam, C.P. / 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 | 8vax.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vax.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vax_validation.pdf.gz | 1010 KB | Display | wwPDB validaton report |
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Full document | 8vax_full_validation.pdf.gz | 1000.2 KB | Display | |
Data in XML | 8vax_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 8vax_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/8vax ftp://data.pdbj.org/pub/pdb/validation_reports/va/8vax | HTTPS FTP |
-Related structure data
Related structure data | 7u87C 7u88C 7u89C 7u8aC 8vawC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4874.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-MG / #3: Chemical | #4: 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: 2.2 Å3/Da / Density % sol: 44.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 35% w/v 1,6-Hexanediol, 50 mM TRIS pH 8.5 75 mM Magnesium sulfate. |
-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: 1.03579 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03579 Å / Relative weight: 1 |
Reflection | Resolution: 1.417→50 Å / Num. obs: 16509 / % possible obs: 91.5 % / Redundancy: 7.2 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.035 / Rrim(I) all: 0.101 / Χ2: 0.953 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 502 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.198 / Rrim(I) all: 0.35 / Χ2: 0.661 / % possible all: 56.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.417→41.944 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.207 / SU B: 1.006 / SU ML: 0.041 / Average fsc free: 0.9699 / Average fsc work: 0.9793 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.077 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: 12.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.417→41.944 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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