+Open data
-Basic information
Entry | Database: PDB / ID: 3ltu | ||||||||||||||||||||
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Title | 5-SeMe-dU containing DNA 8mer | ||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / oligonucleotide / 5-SeMe / selenium / 5-methoxy-uridine | Function / homology | DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | Authors | Sheng, J. / Hassan, A.E.A. / Zhang, W. / Gan, J. / Huang, Z. | Citation | Journal: Chemistryselect / Year: 2023 | Title: Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate Authors: Fang, Z. / Dantsu, Y. / Chen, C. / Zhang, W. / Huang, Z. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ltu.cif.gz | 15.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ltu.ent.gz | 9 KB | Display | PDB format |
PDBx/mmJSON format | 3ltu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/3ltu ftp://data.pdbj.org/pub/pdb/validation_reports/lt/3ltu | HTTPS FTP |
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-Related structure data
Related structure data | 3hg8C 3ijkC 5usaC 5useC 5usgC 5wjrC 1dnsS S: Starting model for refinement 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: 2584.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by solid phase synthesizer. / Source: (synth.) synthetic construct (others) |
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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: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10% v / v MPD, 40 mM Na Cacodylate pH 6.0, 12 mM Spermine tetra-HCl, 80 mM Sodium Chloride, 20 mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2009 / Details: Mirror |
Radiation | Monochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. all: 4766 / Num. obs: 4661 / % possible obs: 97.8 % / Redundancy: 23 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 14.5 / Num. unique all: 446 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DNS Resolution: 1.4→30.46 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.465 / SU ML: 0.03 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.061 / 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: 8.965 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→30.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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