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Yorodumi- PDB-5ux3: RNA hairpin structure containing 2-MeImpG monomer analogue and 2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ux3 | ||||||
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Title | RNA hairpin structure containing 2-MeImpG monomer analogue and 2-MeImp-oligomer analogue | ||||||
Components |
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Keywords | RNA | ||||||
Function / homology | Chem-8OS / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhang, W. / Oh, S.S. / Szostak, J.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ux3.cif.gz | 32.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ux3.ent.gz | 21.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ux3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/5ux3 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5ux3 | HTTPS FTP |
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-Related structure data
Related structure data | 5uz6C 5v0hC 5v0jC 5v0oC 5v9zC 5vcfC 5vciC 5vgwC 6az4C 6bmdC 4fnjS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: RNA chain | Mass: 8238.869 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 2549.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-8OS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68.1 % |
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Crystal grow | Temperature: 292 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 6436 / % possible obs: 98.7 % / Redundancy: 5.1 % / CC1/2: 0.943 / Rmerge(I) obs: 0.08 / Rsym value: 0.067 / Χ2: 1.02 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1 / Num. unique obs: 604 / CC1/2: 0.754 / Rsym value: 0.463 / Χ2: 0.639 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FNJ Resolution: 2.5→44.61 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.957 / SU B: 13.705 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.232 / 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: 77.743 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→44.61 Å
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Refine LS restraints |
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