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Yorodumi- PDB-1n1o: Crystal Structure of a B-form DNA Duplex Containing (L)-alpha-thr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n1o | ||||||||||||||||||
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Title | Crystal Structure of a B-form DNA Duplex Containing (L)-alpha-threofuranosyl (3'-2') Nucleosides: A Four-Carbon Sugar is Easily Accommodated into the Backbone of DNA | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / B-DNA / hydrogen bonding / nucleic acid etiology / tetrose / four-carbon sugar / nucleic acid analogue | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | Authors | Wilds, C.J. / Wawrzak, Z. / Krishnamurthy, R. / Eschenmoser, A. / Egli, M. | Citation | Journal: J.Am.Chem.Soc. / Year: 2002 | Title: Crystal Structure of a B-Form DNA Duplex Containing (L)-alpha-Threofuranosyl (3'-->2') Nucleosides: A Four-Carbon Sugar Is Easily Accommodated into the Backbone of DNA Authors: Wilds, C.J. / Wawrzak, Z. / Krishnamurthy, R. / Eschenmoser, A. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n1o.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n1o.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 1n1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/1n1o ftp://data.pdbj.org/pub/pdb/validation_reports/n1/1n1o | 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: 3649.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase oligonucleotide synthesis was used. #2: Chemical | ChemComp-MG / | #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: 1.75 Å3/Da / Density % sol: 29.04 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: oligonucleotide, sodium cacodylate, magnesium acetate, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol (MPD), pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.978 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. all: 21360 / Num. obs: 21311 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.327 / % possible all: 98.2 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 99.8 % |
Reflection shell | *PLUS % possible obs: 98.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: B-form DNA (native Dickerson-Drew dodecamer) Resolution: 1.2→20 Å
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Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection Rfree: 2130 / Rfactor all: 0.16 / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.16 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |