+Open data
-Basic information
Entry | Database: PDB / ID: 5mrx | ||||||
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Title | 27-nt SRL with a 5-hydroxymethyl cytidine modification | ||||||
Components | RNA (27-MER) | ||||||
Keywords | RNA / modification / tetraloop | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.851 Å | ||||||
Authors | Ennifar, E. / Micura, R. | ||||||
Citation | Journal: J.Org.Chem. / Year: 2017 Title: Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine Authors: Riml, C. / Lusser, A. / Ennifar, E. / Micura, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrx.cif.gz | 59.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrx.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 5mrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mrx_validation.pdf.gz | 399.3 KB | Display | wwPDB validaton report |
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Full document | 5mrx_full_validation.pdf.gz | 400 KB | Display | |
Data in XML | 5mrx_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 5mrx_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrx ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrx | HTTPS FTP |
-Related structure data
Related structure data | 3dvzS 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
#1: RNA chain | Mass: 8774.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MRC=5hydroxymethyl-cytosine / Source: (synth.) Escherichia coli (E. coli) |
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#2: 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: 1.91 Å3/Da / Density % sol: 35.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: well: 3.0M (NH4)2SO4 drop: 50mM KMops pH7.0, 10mM MnCl2, 10mM MgCl2, 1.0mM Na-EDTA pH 8.0, 10mM Tris pH 8.0, RNA 2.5mg/ml 2vol drop + 1vol well |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.77 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.77 Å / Relative weight: 1 |
Reflection | Resolution: 0.85→50 Å / Num. obs: 57106 / % possible obs: 99.6 % / Redundancy: 22.36 % / Rrim(I) all: 0.045 / Net I/σ(I): 30.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3dvz Resolution: 0.851→29.51 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.78
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.851→29.51 Å
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Refine LS restraints |
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LS refinement shell |
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