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Yorodumi- PDB-2dp7: Crystal Structure of D(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dp7 | ||||||||||||||||||
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Title | Crystal Structure of D(CGCGAATXCGCG) Where X is 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / modified nucleotide / 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine / B-DNA | Function / homology | (6-AMINOHEXYL)CARBAMIC ACID / : / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | Authors | Juan, E.C.M. / Kondo, J. / Kurihara, T. / Ito, T. / Ueno, Y. / Matsuda, A. / Takenaka, A. | Citation | Journal: Nucleic Acids Res. / Year: 2007 | Title: Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules Authors: Juan, E.C.M. / Kondo, J. / Kurihara, T. / Ito, T. / Ueno, Y. / Matsuda, A. / Takenaka, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dp7.cif.gz | 29.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dp7.ent.gz | 19.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dp7 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dp7 | HTTPS FTP |
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-Related structure data
Related structure data | 2dpbC 2dpcC 2dqoC 2dqpC 2dqqC 355dS C: citing same article (ref.) S: Starting model for refinement |
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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: 3649.366 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This DNA dodecamer is a synthetic construct. #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Chemical | ChemComp-K / | #5: 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: 2.16 Å3/Da / Density % sol: 42.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20mM sodium cacodylate (pH 6.0), 40mM potassium chloride, 2.5mM magnesium chloride, 1.5mM spermine tetrahydrochloride and 5%(v/v) 2-methyl-2,4-pentanediol (MPD), equilibrated against 45%(v/v) ...Details: 20mM sodium cacodylate (pH 6.0), 40mM potassium chloride, 2.5mM magnesium chloride, 1.5mM spermine tetrahydrochloride and 5%(v/v) 2-methyl-2,4-pentanediol (MPD), equilibrated against 45%(v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→18.836 Å / Num. obs: 10074 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.047 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.55→1.63 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 355D Resolution: 1.55→10 Å / σ(F): 3 / Stereochemistry target values: Maximum Likelihood Details: The value of the item "Number reflections (observed)" is the number of reflections used in refinement. This value excludes the reflections that have sigma(F) less than 3.0.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.55→10 Å
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