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Yorodumi- PDB-5hby: RNA primer-template complex with 2-methylimidazole-activated mono... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hby | ||||||||||||||||||||||||||||
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Title | RNA primer-template complex with 2-methylimidazole-activated monomer analogue-3 binding sites | ||||||||||||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA | Function / homology | Chem-PZG / RNA / RNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.18 Å | Authors | Zhang, W. / Tam, C.P. / Wang, J. / Szostak, J.W. | Funding support | United States, 1items |
Citation | Journal: ACS Cent Sci / Year: 2016 | Title: Unusual Base-Pairing Interactions in Monomer-Template Complexes. Authors: Zhang, W. / Tam, C.P. / 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 | 5hby.cif.gz | 24 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hby.ent.gz | 14.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hby_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5hby_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5hby_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 5hby_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hby ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hby | HTTPS FTP |
-Related structure data
Related structure data | 5dhbC 5dhcC 5hbwC 5hbxC 5krgC 5l00C 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 4167.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
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#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 50.69 % / Description: boat shape crystal |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: Potassium thiocyanate,magnesium chloride,30% w/v Polyethylene glycol monomethyl ether 2,000 PH range: 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2015 |
Radiation | Monochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→50 Å / Num. all: 12711 / Num. obs: 12711 / % possible obs: 93.6 % / Observed criterion σ(F): 0.05 / Observed criterion σ(I): 0.05 / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Net I/av σ(I): 26.5 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.18→1.22 Å / Redundancy: 2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 1.8 / % possible all: 54.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.18→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.571 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0.05 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.288 Å2
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Refinement step | Cycle: 1 / Resolution: 1.18→50 Å
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Refine LS restraints |
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