+Open data
-Basic information
Entry | Database: PDB / ID: 6u6j | ||||||||||||||||||||||||||||
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Title | RNA-monomer complex containing pyrophosphate linkage | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / pyrophosphate | Function / homology | Chem-EQ4 / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Zhang, W. / Szostak, J.W. / Giurgiu, C. / Wright, T. | Funding support | United States, 1items |
Citation | Journal: J.Am.Chem.Soc. / Year: 2019 | Title: Prebiotically Plausible "Patching" of RNA Backbone Cleavage through a 3'-5' Pyrophosphate Linkage. Authors: Wright, T.H. / Giurgiu, C. / Zhang, W. / Radakovic, A. / O'Flaherty, D.K. / Zhou, L. / 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 | 6u6j.cif.gz | 31.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u6j.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 6u6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u6j_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6u6j_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6u6j_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 6u6j_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/6u6j ftp://data.pdbj.org/pub/pdb/validation_reports/u6/6u6j | HTTPS FTP |
-Related structure data
Related structure data | 6c8dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4937.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10mM MgCl2, 1.8 M Ammonium citrate tribasic pH 7.0 |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Aug 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 12495 / % possible obs: 98.9 % / Redundancy: 10.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.059 / Χ2: 0.854 / Net I/σ(I): 44.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1234 / CC1/2: 0.991 / Χ2: 0.388 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6C8D Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 27.78 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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LS refinement shell | Resolution: 1.601→1.642 Å
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