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Yorodumi- PDB-3cjz: Effects of N2,N2-dimethylguanosine on RNA structure and stability... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cjz | ||||||||||||||||||
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Title | Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m22G:A pairs | ||||||||||||||||||
Components | RNA (5'-R(*Keywords | RNA / N2 / N2-dimethyl guanosine / X-ray crystal structure / m22G:A pair / rRNA / tRNA | Function / homology | RNA / RNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | Authors | Pallan, P.S. / Kreutz, C. / Bosio, S. / Micura, R. / Egli, M. | Citation | Journal: Rna / Year: 2008 | Title: Effects of N2,N2-dimethylguanosine on RNA structure and stability: crystal structure of an RNA duplex with tandem m2 2G:A pairs. Authors: Pallan, P.S. / Kreutz, C. / Bosio, S. / Micura, R. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cjz.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cjz.ent.gz | 31.7 KB | Display | PDB format |
PDBx/mmJSON format | 3cjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/3cjz ftp://data.pdbj.org/pub/pdb/validation_reports/cj/3cjz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 4200.595 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: 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: 2.02 Å3/Da / Density % sol: 39.16 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a ...Details: 2ul droplets containing 0.5mM oligonucleotide, 5% 2-methyl -2,4-pentanediol (MPD), 20mM sodium cacodylate, pH 7.0, 6mM spermine-4HCl, 40mM sodium chloride that were equilibrated against a reservoir of 1ml of 35% MPD., VAPOR DIFFUSION, HANGING DROP, temperature 301K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→44.99 Å / Num. all: 6420 / Num. obs: 6027 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3539 / Mean I/σ(I) obs: 4.8 / Num. unique all: 661 / % possible all: 81.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: A cononical A-RNA dodecamer generated with the program TURBO-FRODO omitting U13 and U26. Resolution: 1.8→44.99 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.576 / SU ML: 0.135 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.21 Stereochemistry target values: Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography ...Stereochemistry target values: Standard Refmac parameters and the parameters generated by PRODRG (Schuettelkopf, A. W. and van Aalten, D.M.F. 2004. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr. D Biol. Crystallogr. 60: 1355-1363.) for the residue M2G. 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.807 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→44.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.1389 Å / Origin y: -1.8722 Å / Origin z: 10.7909 Å
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Refinement TLS group |
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