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Yorodumi- PDB-1nzg: Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modifie... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nzg | ||||||||||||||||||
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Title | Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / A-DNA / 2'-modified oligonucleotides | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | Authors | Prhavc, M. / Prakash, T.P. / Minasov, G. / Egli, M. / Manoharan, M. | Citation | Journal: Org.Lett. / Year: 2003 | Title: 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects Authors: Prhavc, M. / Prakash, T.P. / Minasov, G. / Cook, P.D. / Egli, M. / Manoharan, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nzg.cif.gz | 23 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nzg.ent.gz | 14.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzg ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzg | 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
#1: DNA chain | Mass: 3176.178 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: 1.71 Å3/Da / Density % sol: 27.47 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MPD, Sodium Cacodylate, Spermine, Sodium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 8, 1999 / Details: Mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 7031 / Num. obs: 7031 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 6.5 / Num. unique all: 575 / % possible all: 82.9 |
Reflection | *PLUS Lowest resolution: 15 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PARKINSON ET AL.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å
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Refinement | *PLUS Lowest resolution: 15 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |