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Yorodumi- PDB-5ued: RNA primer-template complex with guanosine dinucleotide ligand G(... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ued | ||||||||||||||||||||
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Title | RNA primer-template complex with guanosine dinucleotide ligand G(5')pp(5')G | ||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / dinucleotide | Function / homology | Chem-86S / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | Authors | Zhang, W. / Tam, C.P. / Szostak, J.W. | Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 | Title: Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex. Authors: Zhang, W. / Tam, C.P. / Walton, T. / Fahrenbach, A.C. / Birrane, G. / Szostak, J.W. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ued.cif.gz | 32.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ued.ent.gz | 22.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ued.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ued_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5ued_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5ued_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 5ued_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/5ued ftp://data.pdbj.org/pub/pdb/validation_reports/ue/5ued | HTTPS FTP |
-Related structure data
Related structure data | 5ueeC 5uefC 5uegC 5dhcS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 4500.794 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 53.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.05 M magnesium chloride, 0.2 M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.997 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 15113 / % possible obs: 95.1 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DHC Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.223 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / 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: 18.038 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50 Å
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Refine LS restraints |
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