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- PDB-7kul: DNA modification at 3' end of RNA primer complex with guanosine d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7kul | |||||||||||||||||||||||||||||||
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Title | DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | |||||||||||||||||||||||||||||||
![]() | DNA/RNA (5'-R(*![]() ![]() ![]() Function / homology | DIGUANOSINE-5'-TRIPHOSPHATE / DNA/RNA hybrid / DNA/RNA hybrid (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Fang, Z. / Giurgiu, C. / Szostak, J.W. | Funding support | | ![]()
![]() ![]() Title: Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Authors: Giurgiu, C. / Fang, Z. / Aitken, H.R.M. / Kim, S.C. / Pazienza, L. / Mittal, S. / Szostak, J.W. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.9 KB | Display | ![]() |
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PDB format | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7kukC ![]() 7kumC ![]() 7kunC ![]() 7kuoC ![]() 7kupC ![]() 7lneC ![]() 7lnfC ![]() 7lngC ![]() 5ueeS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: DNA/RNA hybrid | Mass: 4416.824 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 54.49 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol, 50 mM Magnesium Chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.64→50 Å / Num. obs: 13719 / % possible obs: 99 % / Redundancy: 9.6 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.026 / Rrim(I) all: 0.079 / Χ2: 0.953 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 643 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.123 / Rrim(I) all: 0.339 / Χ2: 0.903 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5UEE Resolution: 1.64→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 1.864 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 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: 18.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell |
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