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- PDB-6bmd: RNA hairpin containing GpppG-oligo to mimic intermediate formed b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bmd | ||||||
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Title | RNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper | ||||||
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![]() | RNA / GpppG / helper / intermediate | ||||||
Function / homology | RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, W. / Szostak, J.W. | ||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 66.5 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 412.4 KB | Display | ![]() |
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Full document | ![]() | 420.5 KB | Display | |
Data in XML | ![]() | 6.7 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ux3C ![]() 5uz6SC ![]() 5v0hC ![]() 5v0jC ![]() 5v0oC ![]() 5v9zC ![]() 5vcfC ![]() 5vciC ![]() 5vgwC ![]() 6az4C 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: RNA chain | Mass: 7853.808 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: RNA chain | Mass: 2910.738 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5 |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 7315 / % possible obs: 95.9 % / Redundancy: 4.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.094 / Rrim(I) all: 0.213 / Rsym value: 0.144 / Χ2: 0.654 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 557 / CC1/2: 0.904 / Rpim(I) all: 0.198 / Rrim(I) all: 0.429 / Rsym value: 0.334 / Χ2: 0.571 / % possible all: 74.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UZ6 Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.539 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / 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: 26.407 Å2
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Refinement step | Cycle: 1 / Resolution: 3→50 Å
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Refine LS restraints |
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