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Yorodumi- PDB-1wv6: X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-bu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wv6 | ||||||||||||||||||
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Title | X-ray structure of the A-decamer GCGTATACGC with a single 2'-O-butyl thymine in place of T6, Sr-form | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA | Function / homology | STRONTIUM ION / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | Authors | Egli, M. / Minasov, G. / Tereshko, V. / Pallan, P.S. / Teplova, M. / Inamati, G.B. / Lesnik, E.A. / Owens, S.R. / Ross, B.S. / Prakash, T.P. / Manoharam, M. | Citation | Journal: Biochemistry / Year: 2005 | Title: Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ...Title: Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications. Authors: Egli, M. / Minasov, G. / Tereshko, V. / Pallan, P.S. / Teplova, M. / Inamati, G.B. / Lesnik, E.A. / Owens, S.R. / Ross, B.S. / Prakash, T.P. / Manoharan, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wv6.cif.gz | 21.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wv6.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wv6 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wv6 | HTTPS FTP |
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-Related structure data
Related structure data | 1wv5C 1y7fC 1y84C 1y86C 1y8lC 1y8vC 1y9fC 1y9sC 1yb9C 1ybcC 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: DNA chain | Mass: 3117.111 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-SR / |
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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: 2.66 Å3/Da / Density % sol: 53.79 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.3 Details: SrCl2, PEG400, pH 6.3, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 24, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 2295 / Num. obs: 2295 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 36.576 / SU ML: 0.27 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.448 / ESU R Free: 0.268 / 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: 63.63 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.686 Å / Total num. of bins used: 10 /
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Refinement TLS params. | Method: refined / Origin x: 4.3632 Å / Origin y: 34.0787 Å / Origin z: 3.4322 Å
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Refinement TLS group |
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