+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+58 | ||||||
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Title | Crystal structure of GCC(LCG)CCGC duplex containing LNA residue | ||||||
Components | RNA duplex containing CCG repeats | ||||||
Keywords | RNA / CCG repeats / 5' slippery duplexes / X-linked mental retardation / Huntington's disease / myotonic dystrophy type 1 / LNA Guanosine | ||||||
Function / homology | RNA Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 Å | ||||||
Authors | Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Crystallographic characterization of CCG repeats. Authors: Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e58.cif.gz | 21.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e58.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 4e58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/4e58 ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e58 | HTTPS FTP |
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-Related structure data
Related structure data | 4e59C 3glpS 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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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: RNA chain | Mass: 2528.579 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Similar sequences occur in mRNA in humans / Source: (synth.) Homo sapiens (human) #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: 2.38 Å3/Da / Density % sol: 48.22 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: MES, MgCl2 and Li2SO4, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9148 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9148 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 5762 / Num. obs: 5762 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.3 % / Biso Wilson estimate: 50.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 2.175 / Num. unique all: 273 / Rsym value: 0.673 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GLP Resolution: 1.952→18.79 Å / SU ML: 0.36 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.22 Å2 / ksol: 0.348 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.952→18.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.952→2.1486 Å
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