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Open data
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Basic information
Entry | Database: PDB / ID: 5v0j | ||||||||||||||||||||||||||||
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Title | RNA duplex with 2-MeImpG analogue bound-2 binding sites | ||||||||||||||||||||||||||||
![]() | RNA (5'-R(*![]() RNA | Function / homology | Chem-8OS / RNA / RNA (> 10) | ![]() Biological species | synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Zhang, W. / Tam, C.P. / Szostak, J.W. | Funding support | | ![]()
![]() ![]() 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 KB | Display | ![]() |
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PDB format | ![]() | 23.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ux3C ![]() 5uz6C ![]() 5v0hC ![]() 5v0oC ![]() 5v9zC ![]() 5vcfC ![]() 5vciC ![]() 5vgwC ![]() 6az4C ![]() 6bmdC ![]() 5hbxS C: citing same article ( S: Starting model for refinement |
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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: 4483.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-8OS / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.03 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% MPD, 0.040 M sodium cacodylate pH7.0, 0.012 M spermine tetrahydrochloride, 0.08 M sodium chloride, 0.02 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. obs: 15290 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.041 / Rsym value: 0.045 / Χ2: 0.821 / Net I/σ(I): 35.37 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 744 / CC1/2: 0.804 / Rsym value: 0.5 / Χ2: 0.506 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HBX Resolution: 1.5→84.62 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.737 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.469 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→84.62 Å
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Refine LS restraints |
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