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- PDB-6az4: RNA hairpin complex with guanosine dinucleotide ligand G(5')ppp(5')G -
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Open data
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Basic information
Entry | Database: PDB / ID: 6az4 | ||||||
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Title | RNA hairpin complex with guanosine dinucleotide ligand G(5')ppp(5')G | ||||||
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Function / homology | DIGUANOSINE-5'-TRIPHOSPHATE / ![]() ![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, W. / Szostak, J.W. | ||||||
![]() | ![]() Title: Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide. Authors: Zhang, W. / Tam, C.P. / Zhou, L. / Oh, S.S. / Wang, J. / 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 | ![]() | 34.8 KB | Display | ![]() |
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PDB format | ![]() | 23.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ux3C ![]() 5uz6C ![]() 5v0hC ![]() 5v0jC ![]() 5v0oC ![]() 5v9zC ![]() 5vcfC ![]() 5vciC ![]() 5vgwC ![]() 6bmdC ![]() 4fnjS 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
#1: RNA chain | Mass: 10257.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 2893.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-GP3 / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.3 Å3/Da / Density % sol: 71.6 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 M Magnesium chloride, 0.1 M Sodium cacodylate trihydrate pH 6.5, 1.4 M Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Sep 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.98→50 Å / Num. obs: 4712 / % possible obs: 91.6 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.133 / Χ2: 0.9 / Net I/σ(I): 9.24 |
Reflection shell | Resolution: 2.98→3.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 476 / CC1/2: 0.978 / Χ2: 0.591 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4FNJ Resolution: 2.98→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.839 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.617 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.195 Å2
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Refinement step | Cycle: 1 / Resolution: 2.98→50 Å
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Refine LS restraints |
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