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- PDB-7lnf: 3'-deoxy modification at 3' end of RNA primer complex with guanos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7lnf | |||||||||||||||||||||||||||||||
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Title | 3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | |||||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA / nonenzymatic RNA extension | Function / homology | : / 3'-deoxy-guanosine 5'-monophosphate / DIGUANOSINE-5'-TRIPHOSPHATE / Chem-LCC / Chem-LCG / Chem-LKC / RNA / RNA (> 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 | ![]() | 38.8 KB | Display | ![]() |
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PDB format | ![]() | 25.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.3 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kukC ![]() 7kulC ![]() 7kumC ![]() 7kunC ![]() 7kuoC ![]() 7kupC ![]() 7lneC ![]() 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
-RNA chain , 1 types, 2 molecules AB
#1: RNA chain | Mass: 4422.683 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 8 types, 145 molecules ![](data/chem/img/LCC.gif)
![](data/chem/img/LCG.gif)
![](data/chem/img/GDO.gif)
![](data/chem/img/LKC.gif)
![](data/chem/img/GP3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LCG.gif)
![](data/chem/img/GDO.gif)
![](data/chem/img/LKC.gif)
![](data/chem/img/GP3.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-LCC / [( #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MG / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.02 M Magnesium sulfate hydrate, 0.002 M Cobalt (II) chloride hexahydrate, 0.05 M Sodium cacodylate trihydrate pH 6.0, 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine |
-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: Dec 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 13195 / % possible obs: 99.8 % / Redundancy: 10 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Χ2: 0.935 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 658 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.142 / Rrim(I) all: 0.418 / Χ2: 0.732 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UEE Resolution: 1.652→27.748 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 1.925 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 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: 15.582 Å2
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Refinement step | Cycle: LAST / Resolution: 1.652→27.748 Å
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Refine LS restraints |
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LS refinement shell |
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