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- PDB-7kum: LNA 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: 7kum | |||||||||||||||||||||||||||||||
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Title | LNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G | |||||||||||||||||||||||||||||||
![]() | 5'-R((LCC)P*![]() RNA / nonenzymatic RNA extension | Function / homology | DIGUANOSINE-5'-TRIPHOSPHATE / 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 | ![]() | 37 KB | Display | ![]() |
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PDB format | ![]() | 24.7 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 ![]() 7kulC ![]() 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: RNA chain | Mass: 4444.834 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: 2.77 Å3/Da / Density % sol: 55.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Sodium formate, 50 mM Magnesium chloride |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977408 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→50 Å / Num. obs: 12474 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.013 / Rrim(I) all: 0.054 / Χ2: 0.998 / Net I/σ(I): 52.3 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 17.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 607 / CC1/2: 0.994 / CC star: 0.999 / Rpim(I) all: 0.115 / Rrim(I) all: 0.489 / Χ2: 0.863 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UEE Resolution: 1.714→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.984 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.107 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: 15.717 Å2
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Refinement step | Cycle: LAST / Resolution: 1.714→50 Å
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Refine LS restraints |
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LS refinement shell |
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